Peterborough manager Darren Ferguson is yet to decide whether or not to appeal against Lee Tomlin's red card.
Teenage substitute Macauley Bonne headed in Luke Garbutt's fine cross with 21 minutes remaining on his 18th birthday to secure the injury-hit U's an unlikely win over Posh, who had Tomlin sent off for violent conduct.
Posh striker Tomlin was dismissed eight minutes into the second half after he had been ruled to have kicked out at Colchester's Craig Eastmond.
Ferguson said: "It was a decision by the linesman, who said that Lee kicked out, but I've seen it again and I can't really make my mind up.
"He's just blocked him and there's a collision, but it was a brave decision that you don't normally see from a linesman that far away.
"I've only seen it the once and I'd have to see it again before we decide whether or not we're going to appeal it.
"I thought we were the better team after Lee was sent off and we showed a lot of positivity and energy.
"That was nothing to do with Lee's performance; it was just the way the game went.
"We controlled the game in the first half, but the final pass let us down.
"They were happy to stay in the game, but it was a poor goal to lose and it wasn't anything to do with numerical disadvantage."
Colchester keeper Walker denied Jack Payne and Tommy Rowe in the first half while at the other end, Posh keeper Bobby Olejnik foiled Eastmond, who also hit the crossbar just before half-time.
Peterborough were reduced to 10 men when Tomlin appeared to kick out at Eastmond and was dismissed.
Bonne's winner on his home debut sealed Colchester their first win in 12 league games.