Lisbie's solo strike put Town two up and, although sub Steven Gillespie pulled one back late on, the hosts held on comfortably.
Ipswich had taken the lead through Pablo Counago's first goal of the season on a night when his compatriot Ivan Campo made his debut for the Blues.
The former Real Madrid star played a holding midfield role and showed his class with a string of precise passes.
Ipswich threatened early on with Alan Quinn's shot saved in the opening seconds by Dean Gerken, before Jon Walters headed a Quinn corner over.
Colchester came back into the game and Gareth McAuley had to block a fierce Johnnie Jackson shot, before Phil Ifil and Clive Platt shot wide.
Ipswich went ahead on 28 minutes when Counago's shot from 25 yards squirmed under the hands of Gerken, who will feel he should have saved it.
The keeper atoned soon after with a superb save to tip away Lisbie's goalbound header.
Scott Vernon flicked a shot just wide and Richard Wright dived to save a Mark Yeates free-kick as Colchester rallied after the break.
Quinn nodded over for Town before Lisbie made it 2-0 by dancing past Paul Reid on the left flank and racing clear to curl a shot in off the far post.
Jackson was denied by Wright who then slowed up a Gillespie shot enough for defender Richard Naylor to get back and hook off the line via the crossbar.
Colchester ensured a nervy finale when Gillespie neatly chipped Wright from a tight angle, but he was injured in the process and, with all their subs used, Ipswich played out time comfortably against the ten men.