The U's finished 2008 on a high as they moved into the top half of the table in front of a new record league crowd at the Weston Homes Community Stadium.
It was a tale of two penalties in north Essex as first Steven Gillespie slotted home his spot kick, before Jimmy Walker saved Orient's second half set piece.
The result moved the U's up to eleventh in the table with their fifth win in seven league games and they go into 2009 with plenty of momentum.
Boss Paul Lambert made three changes from the side that defeated Brighton on Friday.
Paul Reid came in for the injured Chris Coyne, whilst there was a new strike duo up front.
Johnnie Jackson was rested onto the bench with a hamstring injury, whilst Clive Platt was also amongst the subs as the U's manager kept to his pre-Christmas promise to rotate during the festive period, with Scott Vernon and Steven Gillespie starting up front.
Gilly was making his first start since the end of October, when the U's beat Carlisle 5-0.
And it was the returning front man who had the first effort on goal after four minutes. Perkins helped the ball into his path and, with a first time effort, he dinked an effort wide of the far post that Morris was happy to watch go on its way.
Nine minutes in and it was his strike partner Vernon who was causing problems, chasing down Morris as the home keeper dealt unconvincingly with a backpass.
Demetriou became the first player to go into the book on twelve minutes, after catching Izzet when the two players went for a header on the halfway line. The home crowd thought it warranted more, but there didn't seem to be too much intent.
The U's were looking solid enough, and whilst looking the more promising going forwards, they were still lacking that magic touch in the final third to break down the Orient back line.
Yeates tried to provide that wizardry on 20 minutes when the U's won a free kick twenty-odd yards from goal. He curled his effort near side, but it was always going just wide of the post.
The U's went closer a minute later as Gillespie sprung the offside trap and kept his composure to bear down on goal. Under pressure from Saah, he got a good shot away but Morris flung himself to his right to save at full length.
The front man was looking dangerous and went close again midway through the first half as a ball was dropped into Vernon on the edge of the box.
He chested down to Gillespie, who with a first time angled effort struck a shot that went just wide of the far post.
There followed a spell where Orient started to get the break on the ball, but the U's were defending stoutly and Gillespie again broke the offside trap on 28 minutes to almost send over a dangerous cross into the box.
The U's did have a touch of fortune on 34 minutes when a Thornton free kick from a central position took a deflection off the wall. Thankfully, Walker had not strayed too far in the original direction of the shot and regained the ball at the second time of asking under pressure from Boyd.
At the other end, a backpass to Morris was undercooked with Yeates steaming in and it was only just got to by the keeper.
A minute later, though, and the U's had a penalty. Hammond seized on a loose ball to surge into the area and his low cross was blocked by the hand of Mkandawire.
The referee pointed to the spot and Gillespie made no mistake as he sent the keeper the wrong way to give the U's the lead.
Another handball not long afterwards saw Thornton go into the book on 41 minutes, but it was for his protests to the official that the card was given.
A yellow card was issued to a player from either side at the start of the second half, with Jarvis and Tierney both being booked by the referee for fouls on the West Stand side of the pitch.
The U's retained the upper hand and nearly grabbed a second eight minutes after the restart. Hammond switched it out right to Maybury, who dropped it back to Perkins. His fizzing cross was just missed by Izzet steaming in at the far post.
Then controversy followed. A free kick was thrown into the box and as Parkin went to control, it hit Reid at close range. The away fans appealed for handball and, after a delay, the referee pointed to the penalty spot.
Protests followed by the home players to no avail, but the disappointment soon turned to delight from a Colchester perspective as Walker started to dive the wrong way but twisted his body back to parry the ball away from danger.
The game had stepped up in intensity now with tackles flying in everywhere as the two teams looked to try and strengthen their respective positions in the match.
Fifteen minutes into the second half and the U's put together some good play down the left with Tierney and Yeates doing well, before the latter sent over a dangerous cross that Vernon flicked a looping header over the bar.
The visitors were the ones starting to have some joy though, particularly down the U's left and that encouraged Martin Ling to make two changes with 65 minutes on the clock.
Morgan and Dawkins came on to give the visiting side fresh impetus, but the two players first touches weren't the best - Dawkins kicking the ball straight out of play and Morgan losing the ball before fouling Hammond.
The U's made their own double change midway through the second half, with Gillespie and Izzet making way for Jackson and Platt.
The visitors pressure continued, though, but it was the U's who were next to threaten the goal. Tierney surged forwards thirty yards and although his cross cut out the defenders, Platt slipped and then Vernon couldn't work the ball out from his feet to get his shot away.
Morgan then went into the book for a foul, before the U's completed their subs by bringing on White for Yeates for the last fifteen minutes - Maybury pushing up into right wing as he had done on Boxing Day.
Chambers became the latest to be booked for a foul on the newly introduced right back, before a fracas in the middle of the park with nine minute remaining saw the ref pull the game short to deal with the fall-out.
Thornton was the man to see red for his part in the disagreement and the visitors would play the last eight minutes a man short. And indiscipline continued when Melligan kicked the ball away to become the latest to go into the book.
The U's then could have closed out the game with three minutes remaining.
White thrust the ball into the area, Perkins headed back across goal which looked like it was going wide until Vernon helped it back into the danger area across the line with a shot from the narrow angle.
Morris scooped it upwards and Chambers headed off the line, only for Perkins to head back towards goal, with his effort beating the man on the line but coming back off the post.
Four additional minutes were added, the visitors having a series of corners at the death to try and get back into it.
But the U's remained resilient as they reversed the FA Cup score to move into the top half of the table.
U's: Walker, Maybury, Tierney, Baldwin, Reid, Yeates, Izzet, Hammond, Perkins, Yeates, Gillespie, Vernon
Subs: Gerken, White, Wordsworth, Jackson, Platt
We will have all of the action from the match live on U's World with our friends from BBC Essex.
To tune into the game, click HERE from just before 3pm.

















