The U's struck two goals inside six minutes in the second half to secure League one football next season and earned themselves a standing ovation from the home fans.
Gavin Massey forced in the opener and defender Tom Eastman's 71st-minute far post header proved the clincher for the U's who had to get at least a draw to stay up.
Abbott said: "It was not the way we wanted to finish. It's been a long, tough road, but we did the hard work over the last seven games.
"The players were flat. We wanted to go out on a high, but we could not find the fluency and the bit of quality we needed.
"Colchester got a couple of scrappy goals and that put a damper on things.
"There's a lot of work to be done. It didn't look like we needed major surgery over the previous six games, but in this we did.
"We want to be better than mediocre and we didn't send our fans home happy."