In-form striker David Mooney grabbed his fifth goal of the campaign as Kevin Lisbie also found the net for Russell Slade's team to ensure the visitors would remain top of League One.
Colchester had been unbeaten going into that game, and they were joined in losing that record by Peterborough United, who came up short at London Road against Crawley Town in the first-ever meeting between the sides.
Crawley ran out 2-0 winners with veteran Gary Alexander finding the net on both occasions while the hosts, who had averaged three goals-a-game ahead of the fixture, failed to notch.
However, Crawley's performance was overshadowed by the sending off of Michael Jones for two bookable offences.
Elsewhere, Mark Cooper's Swindon followed up their midweek League Cup win over QPR by putting five past Crewe Alexandra at home, with Nile Ranger grabbing his second goal in as many games.
And Brentford could only take a 0-0 draw from their clash with Carlisle at Brunton Park, despite Greg Abbott's side having yet to win a game this term.
Rock-bottom Coventry CIty moved closer to wiping out their ten-point penalty as they earned a 1-1 draw against Shrewsbury Town away from home.
At the other end of the table, high-flying Bradford City remain undefeated after Kyal Reid's free-kick cancelled out Greg Tansey's first-half penalty in a 1-1 draw with Stevenage.
Wolves fans were also treated to a successful away trip as they beat Port Vale 3-1, with Leigh Griffiths, Bjorn Sigurdarson and Kevin McDonald all netting inside the first 27 minutes.
But there was more disappointment for Sheffield United, who conceded an 87th-minute Antony Kay goal to suffer a 1-0 defeat to MK Dons at home.
In other matches, Notts County succumbed to their fifth defeat of the season, losing 1-0 to Rotherham, while Tranmere took a first victory of the campaign against Oldham Athletic and Bristol City drew away to Gillingham.
Preston North End, meanwhile, put three unanswered goals past a hapless Walsall side at Bescot Stadium.
