Manager Peter Taylor asked for another fast start from Albion after last Saturday's win against Oldham.
Instead it was the visitors who had a great chance to take the lead in the second minute.
Mayo slipped as he tried to deal with Stockwell's cross. It presented Rapley with a clean opening eight yards out, but he shot too close to Kuipers.
Mayo was a little unfortunate, but Rapley will feel he should have added to his tally of seven goals since a summer move from Notts County.
Morgan required treatment after coming off worst in an aerial chance with Colchester's leading marksman McGleish five yards inside the Albion half.
Albion went ahead slightly against the run of play in the 16th minute.
One of Watson's trademark quick free kicks from the right flank was toe-poked in by Zamora from close range.
Zamora's 11th goal of the season yet again demonstrated the telepathic understanding he has with Watson in such situations.
It also ended his longest scoring drought at Withdean, spanning five matches.
Gavin Johnson collected the first caution of the contest in the 26th minute for a crudely mistimed tackle on Hart just inside Albion territory.
Colchester, one of the surprise packages of the season so far, were still looking quite dangerous going forward.
The crowd felt most of referee Messias' decisions were going against the Seagulls and their mood was not helped when Morgan was booked on 35 minutes for having too much to say when Hart had been penalised for a foul.
Kuipers, making his 50th League appearance for the Seagulls, continued to be the busier of the two keepers.
The big Dutchman was called into action again to keep out a shot by Izzet from the edge of the area after Carpenter had given away possession to the United midfielder.
Kuipers excelled himself again in first half stoppage time. He smothered McGleish's effort from an acute angle from a cross by Izzet as Albion looked in vain for an offside flag.
The half ended with a shot well over the bar from the Seagulls skipper Oatway when he was set up by Zamora.
Albon were forced into a change for the second half.
Morgan had not fully recovered from the early whack in the face he received from McGleish, so Crosby took over at the heart of the defence.
The Seagulls desperately needed the security of a second goal and they almost got it in the 52nd minute.
Wicks converged on a cross from Oatway with a Colchester defender and keeper Woodman.
The ball rebounded off the Seagulls' stopper's shoulder for Steele to hook a left-foot volley over the bar.
Colchester continued to enjoy the lion's share of the possession, a state of play Albion fans have been unaccustomed to at Withdean.
The visitors made a substitution on 62 minutes, Keith replacing French youngster Pinault in midfield.
Albion made a second change on 64 minutes, Brooker replacing Steele. The decision did not meet with the approval of supporters, who seemed to be expecting Jones to be taken off in a straight swap.
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