The Eagles had not won in their previous nine games, but they benefited from a terrible start by the home side which sent them on their way to a second away victory of the campaign.
Clinton Morrison was the hero with both goals. The Palace striker had scored his 100th goal for the London club in the previous match against QPR, and it took him only six minutes to net his 101st and therefore break the deadlock.
James Scowcroft was the creator as he sprung the offside trap to deliver a low cross for his strike partner Morrison to sweep home from close range.
It got even worse for the U's two minutes later when centre-half Pat Baldwin was sent off for a professional foul on Paul Ifill, who was clean through on goal.
United therefore had to play the final 82 minutes with just ten men, and already a goal down.
To their credit, the home side then took control and had several chances to equalise before half-time.
Twice striker Kevin Lisbie was denied by excellent saves by Julian Speroni. The Argentinian keeper turned away Lisbie's goal-bound shot on the half-hour mark, and also denied the ex-Charlton striker from the ensuing corner.
Ten-man Colchester deservedly drew level in the 69th minute thanks to a second goal of the season for Johnnie Jackson.
Ex-Tottenham midfielder Jackson latched on to a fine pass from Mark Yeates to beat Speroni with a fierce left-foot shot, the ball rolling in off the far post.
But Colchester's joy was short-lived. Just five minutes later Morrison headed home his second goal of the game, which this time proved to be the winner.
Home keeper Dean Gerken seemed to be impeded when trying to intercept a headed delivery from Shaun Derry, but no foul was given as Morrison gleefully nodded home from the edge of the six-yard box.