Theo Robinson put Vale ahead on nine minutes with his first goal for the club, firing home from 12 yards.
Bottom club Colchester struggled to test the home side, Vale keeper Chris Neal comfortably holding substitute Nathan Oduwa's shot in the second half.
Vale made the points safe when substitute Byron Moore crossed for Sam Foley to head in off the crossbar.
Much-travelled former Derby striker Robinson, signed on a free transfer from Motherwell at the end of January. was only playing because of 11-goal top scorer A J Leitch-Smith failing a morning fitness test on a hamstring injury.
Port Vale manager Rob Page told BBC Radio Stoke:
"Sometimes it isn't going to be pretty or go to plan. Sometimes you have to go off the cuff a little bit.
"I am really pleased for Theo Robinson because it has been a frustrating time for him since he has come in.
"Every striker wants to score goals for confidence for themselves. And he has worked his socks off. It has been a big ask of him because he is not an out and out target man."
Play-off hopefuls Port Vale stretched their unbeaten home League One record to 14 games by beating Colchester.