Louis Lancaster's young Bees conceded twice in the the final quarter of an hour as they were denied a first victory of the season at Florence Park.
Josh Stockwell's curling effort had given The Bees a 15th minute lead before Macauley Bonne equalised 13 minutes later.
Courtney Senior restored The Bees lead with his first touch after replacing Stockwell, but late on Bonne grabbed his second before the impressive Jack Simmons scored the winner with six minutes to go.
With Joe Taylor away with the New Zealand Under 17s James Bransgrove started in goal but otherwise it was an unchanged starting XI from the defeat against Barnet.
Colchester started brightly and forced Bransgrove into an excellent save after five minutes. Bonne beat Max Herbert to a bouncing ball and squared for Nnamdi Nwachuku whose deflected shot was turned around the post by Bransgrove.
From the resulting corner George Pilbeam had to be alert to clear Bonne's header off the line.
The home side thought they had broken the deadlock in the ninth minute when Nwachuku converted Simmons teasing cross but the linesman had his flag raised for off-side.
Brentford were struggling to get any foothold in the game but they took the lead with their first attack. Michael Onovwigun won the ball in midfield and held off two challenges before finding Stockwell. The Bees striker was allowed to wander into the Colchester half before having time to pick his spot and curl in a sublime effort from 25 yards.
Despite falling behind Colchester kept pressing and should have levelled nine minutes later. Nwachuku broke through the middle but tamely hit his shot straight at Bransgrove. Bonne picked up the rebound but Stefan Tomasevic managed to get back on the line to turn it behind for a corner.
Bonne was not as wasteful four minutes later when good work by Simmons on the left wing found him unmarked on the edge of the six yard box. He gave Bransgrove no chance with his powerful header.
Simmons was a constant thorn in the Bees side and he set up Nwachuku with a clever reverse pass but the tall striker's shot from a tight angle was easily dealt with by Bransgrove.
Moments later Ryan O'Donoghue advanced from left-back and looked to try his luck from 30 yards but his shot skimmed off Tomasevic's head and behind for a corner.
Colchester continued to press and had a golden chance to take the lead into half-time. Thomas Lapslie was given time to slip in Jack Curtis but the midfielder screwed his shot wide from twelve yards with only the keeper to beat.
The second half followed on in a similar vein to the first half with plenty of energy and endeavour but a lack of precision in the final third.
It took until nearly the hour for the first action of note in the second half with Pilbeam's low shot being easily saved by Gines Guzman Rosique in the Colchester goal.
Louis Lancaster shuffled his pack on the hour replacing Stockwell with Senior and it paid instant reward for The Bees.
Rosique took far too long on the ball and Senior was able to nip in and take the ball away from him before rolling home into an open net.
Colchester came looking for an equaliser and Bransgrove had to alert to keep out Curtis's acrobatic effort after Lionel Stone had blocked Nwachuku's shot.
The home side grabbed an equaliser in controversial circumstances with a quarter of an hour to go.
Simmons' cross was half-cleared and Curtis fed Bonne in the penalty area. Both sides seemed to stop waiting for an off-side flag that never came. Bonne took his time and rolled the ball into the bottom corner to level the scores.
Colchester kept pressing and it was fitting that their winner was scored by the highly impressive Simmons but it was another goal that Brentford won't want to watch again.
Substitute Milenge let a hopeful pass slip under his foot releasing Simmons. Simmons backed Milenge into the penalty area before firing across Bransgrove. Although Bransgrove got a hand to the shot he was unable to keep the effort out.
Brentford pushed Tomasevic up-front to try and grab a share of the spoils but that left spaces at the back which Colchester should have exploited.
Firstly Nwachuku was denied brilliantly one-on-one by Bransgrove and then Nwachuku chose to shoot with Bonne un-marked on the edge of the area.
In the end it didn't affect the scoreline as Colchester held out to maintain their position at the top of the table.
Colchester United : Gines Guzman Rosique; Callum Rogers, Billy Roast, Frankie Kent, Michael O'Donoghue; Jack Curtis, Thomas Lapslie, Sam Szmodics, Jack Simmons; Nnamdi NwachukuSubs not used: Joe Morris, Conor Clarke, Matthew Brown, Tyler Brampton
Goals: Macauley Bonne 28, 74; Jack Simmons 84
Brentford: James Bransgrove; Richard Bryan, Lionel Stone, Stefan Tomasevic, Max Herbert (sub Fabien Rowe 85 mins); George Pilbeam, Michael Onovwigun, Lewis Lavender, Walter Figueira (sub Gradi Milenge 71 mins); Josh Stockwell (sub Courtney Senior 60 mins), Myles Hippolyte
Subs not used: Joe Maloney
Goals: Josh Stockwell 15; Courtney Senior 61