Scott Vernon struck a goal in each half for lowly Colchester to deal a blow to Ipswich's play-off hopes.
The forward ended a run of 10 games without victory, firing into the bottom corner from 12 yards on 29 minutes.
Ipswich were purposeful and Danny Haynes spurned an decent opportunity to equalise just before the break.
But Colchester wrapped up the points 17 minutes from time with another assured finish from Vernon finishing right into the corner from the edge of the area.
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