Vernon struck twice one in either half to chalk up the U's first win in 11 games. And at the same time, keeper Dean Gerken made a couple of excellent saves to help record his club's first clean sheet in the last 40 games.
In fact, it was only Colchester's second clean sheet of the season.
Visiting Ipswich dominated possession and created plenty of chances, but they were made to pay by Vernon's killer instinct in front of goal.
Alan Lee was the main culprit for Town because he missed several of the best opportunities. Lee had a couple of headers saved by the excellent Gerken, before Vernon struck with the opening goal in the 29th minute.
Kevin Lisbie controlled a long through ball from John White and then squared into the path of Vernon, who burst past defender Alex Bruce before calmly slotting the ball beyond on-rushing keeper Stephen Bywater.
Town could find no response before the break, even though Danny Haynes had a goal ruled out for offside when he diverted home a volley from Alan Quinn in the last minute of the first half.
Ipswich's poor away form could well see them miss out on a play-off spot come the end of the season and although they continued to dictate after the break, it was Colchester who scored again with Vernon killing off the game in the 73rd minute.
Ex-Blackpool striker Vernon shrugged off the challenge of Luis Castro Sito before trying his look with a left-footed shot from just inside the box which rolled in off the far post.
There was no way back for Ipswich, and the U's could have scored again in the closing minutes.
Livewire Lisbie was narrowly off-target with a couple of shots on the break while Bywater did well to beat away a goalbound stride by Phil Ifil.