The Terriers fought back after conceding an early goal to record an important win at the Matchroom Stadium, with goal-scoring sensation Jordan Rhodes breaking the Club's all-time record for League goals in a single season.
Former Leeds midfielder Matt Spring gave the hosts an early lead with an impressive strike, but Rhodes soon levelled matters and the Terriers went on to dominate first-half possession.
The Scottish international then took centre stage, showing great predatory instinct to put his side ahead before the interval before notching his 35th League goal of the season to secure the three points in the final minute of the game.
The blue and white stripes of Town were well backed by the vocal away support as the game kicked off in South East London and forced the first corner of the game in the fourth minute when Jack Hunt got forward to send a deflected volley behind former Town 'keeper Paul Rachubka's goal.
That set piece came to nothing, but minutes later Danny Ward showed he had the legs on right back Terrell Forbes. After outpacing the Orient defender down the touchline it took a challenge from covering centre half Ben Chorley to clear the danger, but still the signs were encouraging.
Lee Novak - operating on the right flank on the evening - then tried his luck after collecting a half-cleared Morrison long throw around 25 yards out, but his effort drifted well over Rachubka's crossbar.
Home striker David Mooney headed Orient's first corner of the game high and wide in the 13th minute.
GOAL - Leyton Orient then took an early lead with their first shot at goal in the 14th minute. A George Porter long throw from the Town left was not properly cleared and when the ball was cleared to the edge of the box central midfielder Matthew Spring hit an excellent half-volley from around 20 yards, giving Alex Smithies absolutely no chance in the Town goal.
The Terriers tried to fight back immediately and created a decent opportunity two minutes later when Novak flicked the ball across the face of the box, but fellow wide-man Ward dragged his shot badly wide of the target when in a decent position.
GOAL - Town did hit back only three minutes after going behind when Jordan Rhodes collected a loose ball in the box and skillfully back heeled the ball into the net - the effort took a deflection off Jimmy Smith before resting in Rachubka's goal. Ward played the set-piece towards the near post where Alan Lee was on hand; his effort was blocked by a defender but fell to Rhodes, whose clever back-heel towards goal from the penalty spot hit the Orient player on its way into the net.
Simon Grayson's men continued to press following the equaliser and Ward sent a fizzing 20th minute free-kick into Rachubka's hands with skipper Peter Clarke looking for a goal.
The game was being played in Orient's half for large periods, with home striker Mooney often a lonely figure in attack against the power of Morrison and Peter Clarke. At the other end of the pitch the tenacious Alan Lee was being doubled up on by Leacock and midfielder Smith in aerial challenges, but was doing admirably.
Town almost took the lead for the first time in the game on the stroke of 29 minutes when Novak won yet another corner down the right side. Ward's ball was to the back post this time, where Peter Clarke rose above his marker to head towards goal; unfortunately for the Terriers, goal-scorer Spring was on the post and cleared to safety.
BOOKING - Jack Hunt picked up his tenth yellow card of the season in the 33rd minute of the season after bringing down Mooney from behind. The young right back now faces a two game ban, ruling him out of the Sheffield Wednesday and AFC Bournemouth games.
Like Carlisle on Saturday, Orient's formation meant they had an extra man in the centre of the park and often Smith was dropping deep to try and gain possession. However, Russell Slade's side were still being pressed back into their own half for large periods.
BOOKING - Alan Lee followed Jack into the book in the 42nd minute with a rash challenge on left back Dickson after the big Irishman stood on the ball to gift the defender possession - after doing brilliantly to hold it up initially.
GOAL - Town then took the lead through another set piece in the two minutes of first half added time, with Jordan Rhodes netting his 37th goal of the season. With little time left in the half Sean Morrison was called forward to launch a long throw into the box; Lee did brilliantly once again to flick the ball on with his head at the near post and Rhodes showed his predatory instinct to get across the front of his marker and prod the ball home at close range.
There was still time for left back Dickson to fire a late free-kick into the Town defensive wall.
HALF TIME: LEYTON ORIENT 1 HUDDERSFIELD TOWN 2
SUB - Town made a double substitution during the interval; Lee Novak was replaced on the right by Scott Arfield, whereas Calum Woods replaced the booked Jack Hunt. Novak looked to be carrying a knock towards the end of the first period, whereas the full-back change saw Woods move to the left and Tom Clarke to the right.
Town started well in the second half, with Rhodes breezing past defender Ben Chorley down the left channel; he squared the ball across the box for new substitute Arfield, but his effort was blocked well by Dickson.
BOOKING - Jimmy Smith was the first Orient player to see a yellow card in the 51st minute; after he tripped Diego Arismendi, he was booked for persistent fouling.
Mooney bent a cross straight into the hands of Smithies before Town counter-attacked, with the big clearance up field falling to Rhodes in the left corner. Strike partner Lee brought his eventual cross down at the back post, but ambitiously volleyed wide.
Rhodes and Arismendi soon launched a fantastic move forward that almost resulted in another goal for the prolific Scotland international just before the hour mark. Diego forced Matthew Spring into an error and almost immediately found Rhodes with a pass forward; Rhodes played the ball right as the Uruguayan continued his run forward and the Stoke City loanee picked out Jordan with his cross, only for the striker to head over the bar.
SUB - Orient boss Russell Slade made his first substitution in the 57th minute, with midfielder Marc Laird replaced by veteran striker Kevin Lisbie.
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Almost immediately Lisbie was involved in an attack, rolling Peter Clarke before setting George Porter free down the left. However, just as the Orient man entered the area he was denied a shooting chance courtesy of a superb sliding challenge from Sean Morrison.
Town's travelling faithful were in superb voice as the final half hour commenced in the pouring rain at the Matchroom Stadium and the lively Arfield was the next to try his luck from range, but he blazed well over the bar after collecting a knock-down from Rhodes.
Fellow sub Woods then picked out Ward with a superb cross-field pass in the 70th minute, but the winger rather wasted the crossing opportunity with men to aim at in the box.
The o's were enjoying their best spell of possession at this stage and forced a couple of corners; from one of these Dean Cox deliveries Lisbie flicked a header wide under heavy pressure from his marker Kay.
Another corner was laid back into the path of Spring, who tried to place the ball home; Arismendi stuck a foot out and deflected the ball inches wide of Smithies' right-hand post.
SUB - Town manager Simon Grayson made his final substitution of the evening in the 78th minute, with Danny Cadamarteri replacing workhorse Lee.
This change saw Town match up Orient's formation in the final stages, with Cadamarteri moving out to the right and Arfield joining Arismendi and Kay in the middle.
SUB - Orient made a like for like replacement two minutes later, with striker Calvin Andrew replacing Mooney.
Cadamarteri linked up with the impressive Tom Clarke down the right with five minutes left, the pair exchanging passes before the right back finally crossed to the near post. Jordan Rhodes was there in typical fashion, but his marker got a foot to his shot and the ball looped into Rachubka's arms.
GOAL - Jordan Rhodes netted his second goal of the evening in the final minute of normal time to secure the points for the Terriers, breaking the Club's all-time League goals in in one season record surpassing George 'Bomber' Brown and Sammy Taylor. His 36th League goal started with a big clearance up field from Alex Smithies; Danny Cadamarteri challenged for the ball and it ended up infield with Rhodes, who cleverly side-stepped the first challenge before prodding the ball past Rachubka with absolutely no back-lift from around 10 yards out.
FULL TIME: LEYTON ORIENT 1 HUDDERSFIELD TOWN 3
Town's team (4-4-2):
Alex Smithies; Tom Clarke, Peter Clarke (c), Sean Morrison, Jack Hunt (Calum Woods 46); Danny Ward, Diego Arismendi, Antony Kay, Lee Novak (Scott Arfield 46); Alan Lee (Danny Cadamarteri 78), Jordan Rhodes
Ian Bennett, Gary Roberts
Town bookings: Jack Hunt (33); Alan Lee (42)