Yann Songo'o's second half effort sealed all three points for the Shrimps, after Michael Folivi had levelled for the U's, following John O'Sullivan's opener.
Steve Ball lined up with three changes to the eleven that started the game against Cambridge on Tuesday night.
Miles Welch-Hayes, Luke Norris and Kwame Poku were all named as substitutes on the bench, with their starting places taken by Junior Tchamadeu, Michael Folivi, and the U's top scorer, Jevani Brown.
The U's found themselves on the back foot early on with the Shrimps applying the pressure in the opening ten minutes, with Derek Adams' side taking the lead after eight minutes.
John O'Sullivan was the man on target for the visitors when Noah Chilvers' header cleared the ball from a corner. The Morecambe midfielder struck the ball sweetly, as it arrowed in to the back of the net through a crowded penalty area.
The Shrimps were definitely the team on top at the JobServe Community Stadium for the first twenty minutes. Yann Songo'o tested Gerken with a downward header from a corner, with Cole Stockton blasting the ball in to the side netting from a Wildig through ball.
But the U's grabbed themselves an equaliser with twenty-four minutes played and it was Michael Folivi getting himself on the scoresheet for the second game in a row. He got his head to the ball, flicking it towards the far corner. The ball seemed to take a slight deflection off Cole Stockton, but the U's man wheeled away in celebration, levelling the scores.
From then on, Steve Ball's side looked the better of the two teams in the first half. They were comfortable in possesion and keen to get forward at any point, limiting Morecambe's opportunities.
Noah Chilvers drove a low cross into the area after finding space on the right wing, with Davis tapping the ball behind for a corner, narrowly missing the far post, with Folivi lurking ready to feed on any scraps.
When Morecambe did get a chance to retake the lead, Dean Gerken was in the way. Aaron Wildig's low effort was spilled by Gerken, with Carlos Mendes Gomes arriving for the rebound, but the U's 'keeper made up for his intial error by pulling off a brilliant save to push the ball onto the post, with Tchamadeu clearing.
The scores remained level until the two teams headed for the dressing rooms at half time.
Morecambe came out for the second half and almost retook the lead within three minutes. Cole Stockton was played through by second hald substitute Diagouraga and opened his body up to curl the ball into the far corner, but couldn't quite find the angle as the ball bounced off the post and away.
It was an end to end opening few minutes with Stockton denied once again a minute later. Dean Gerken's stunning reaction save started the counter attack for the U's with Bramall and Folivi taking the ball up the other end and testing Halstead before the Shrimps were able to clear.
And the visitors came again at the U's defence, with Gerken denying Stockton with his feet this time and managing to get the ball away from the danger area.
Morecambe hit the bar for the second time in ten minutes, striking the bar this time. Toumani Diagouraga was the man with the effort, as he got his head to the ball, and beat Gerken but not the woodwork as the U's held on at the back.
The visitors, perhaps deservedly, got their noses in front once again with sixty-one minutes on the clock. Diagouraga flicked the ball on from a corner, with Yann Songo'o arriving at the back post to tap the ball into the net and make the score 2-1.
It could have been level five minutes later, when Poku's cross seemed to catch out Halsetad. The ball looped over the 'keeper who just managed to get fingertips on the ball and touch it onto the woodwork, before the ball bounced out with no U's players able to convert.
It started to look like it wasn't to be for the U's as they pushed and pushed to get an equaliser. Michael Folivi almost grabbed a second of the game, when he dug out a shot from outside the area that was arrowing into the top corner, but Halstead got across to save well.
The Shrimps' 'keeper did well in stoppage time to deny a late equaliser from Ben Stevenson, as he tried his luck from distance, but he couldn't break through.
Dean Gerken pushed up for a corner deep into stoppage time, but with the extra man, the U's couldn't get through and grab a late goal as they fell to a first league defeat of the season at the JobServe Community Stadium.
Steve Ball's side drop out of the play-offs with the defeat and fall to tenth position, remaining on twenty-eight points. Next up for the U's is the Essex derby, when the U's travel to Southend United on Boxing Day.
Colchester United starting XI: Gerken, Bramall, Smith, Senior, Brown (Norris 60'), Harriott (Poku 60'), Chilvers (Gambin 66'), Eastman, Stevenson, Tchamadeu (Welch-Hayes 60'), Folivi.
Unused subs: George, Sowunmi, Clampin.
Morecambe starting XI: Halstead, Hendrie, Lavelle, Davis, Stockton, Wildig (Gibson 90'), Mendes Gomes, O'Sullivan (Kenyon 90'), Phillips (Diagouraga 46'), Cooney, Songo'o.
Unused subs: Turner, Knight-Percival, Leitch-Smith, McAlinden.
Attendance: 1,094