The O's looked more threatening in the second period and were furious at referee Mark Heywood as they had a goal disallowed and four penalty appeals turned down.
Fabio Liverani handed debuts to both Neal Eardley and Ryan Hedges whilst their were returns from injury also for Romain Vincelot and Dean Cox. Scott Cuthbert and Kevin Lisbie were absent for the trip across Essex through injury though the Orient players were boosted by a large travelling contingent on a chilly afternoon in Colchester.
It was also a return to a 4-4-1-1 formation as David Mooney shifted back to his more usual position just behind the in-form Chris Dagnall.
The home side looked the more dangerous in the opening stages and Gary Woods was called into action early on to make a brave stop at the feet of Chris Porter.
It was a let off for the O's but soon after they would not be so fortunate when a cross found its way to the lurking Gavin Massey at the back post who smashed home to give the U's a lead.
Orient were far from at their best but started to grow into the game following the goal as the lively looking Hedges tested the hands of Sam Walker with a bending effort from distance.
They would be gifted a better opening after 26 minutes when Mooney grabbed possession on the corner of the box but dragged his shot wide.
In truth it was far from a memorable half as the sun disappeared and the temperature dropped though Hedges remained the O's most dangerous outlet as the half neared its conclusion. First he sent in a dangerous ball that flashed wide of the post before a minute later releasing Romain Vincelot who stood up a dangerous ball to the back post which just evaded Dagnall and Mooney.
There were signs of encouragement as the half wore on but the second half got underway in disastrous fashion as Colchester doubled their lead when Kaspars Gorkss rose highest to nod home from a corner.
It almost got worse a minute later when Colchester debutant Porter latched on to a clearance and rounded Woods before Nathan Clarke made a brilliant saving tackle to deny him.
As we approached the hour mark Orient again were enraged by a handball that was not given when Cox had a shout deflected wide. From the resulting corner Vincelot went close with a header but time was ticking away against the O's.
On came Gianvito Plasmati in place of Mooney and soon after Orient thought they had found a way back into it. Cox found space on the left and crossed brilliantly for Dagnall to head home from six yards but it was ruled out for offside.
Orient were laying on the pressure and had a third penalty appeal waved away when Vincelot went down under pressure from Gorkss in the box but not much seemed to be going their way heading into the closing stages.
Vincelot had been Orient's stand out performer with a swashbuckling second half performance and he was caught late and very high by Elliot Hewitt with 10 minutes to go and the United player was sent off.
A fourth penalty appeal for another handball was turned down before a minute later John Lundstram had a low shot brilliantly saved.
It was not their day though as the 1777 travelling fans headed home disappointed.
ORIENT: Woods, Sawyer (Dossena 88), Vincelot, Cox, Mooney (Plasmati 64), Lowry, Clarke (C), Dagnall, Lundstram, Hedges, Eardley
SUBS: Omozusi, Lee, Wright, Grainger, Dossena
BOOKINGS: Vincelot 75
COL U: Walker, Gorkss, Briggs, Eastman, Clohessy , Massey (Gordon 86), Szmodics (Moncur 84), Lapslie, Fox, Hewitt, Porter (Bonne 90)
SUBS: Lewington, Watt, Marriott, Sembie-Ferris
GOALS: Massey 14, Gorkss 48
BOOKINGS: Eastman 44, Szmodics 75
RED: Hewitt 83
Att: 5668 (1777)