After a first half of few chances, the game really burst into life when the U's took the lead on 50 minutes thanks to Clive Platt's eighth goal of the season.
City keeper Adriano Basso could not hold on to a stinging drive from winger Kevin McLeod and there was striker Platt to sweep home the rebound for his first goal of 2008.
But Colchester's lead only lasted for 90 seconds, which is all it took for Dele Adebola to nod home the equaliser.
Adebola rose above the U's defence to head home a cross from Jamie McAllister, and the Robins never looked back.
They grabbed what proved to be the winner on 58 minutes when catching the home team out with a quickly-taken free-kick.
Michael McIndoe's long-range shot took a wicked deflection off a home player as the ball looped over stranded keeper Dean Gerken and into the roof of the net.
The visitors did suffer a setback when right-back Bradley Orr was sent off with 11 minutes remaining.
Orr had been booked in the first half for a foul on McLeod, and he was then shown a second yellow and ensuing red card for kicking the ball away after committing another foul.
However, Colchester could not make their numerical advantage count during the closing minutes as Bristol City held on to return to the top two and an automatic promotion slot.
Their manager Gary Johnson believes that promotion will be theirs if they can win seven of their last 12 fixtures, while Colchester face a very different task at the other end of the table.
The Essex club are second from bottom and four points adrift of safety. They played well for 50 minutes against City, but faded badly from then on.
Their cause was not helped by injuries to defenders John White (dislocated elbow) and Chris Coyne (concussion), who both took no part in the second half.