A slow start by the home side was capitalised upon by Colchester as former Stoke City forward Chris Iwelumo proceeded to intimidate the Vale defence.
However, his finishing was somewhat embarrassing when, after five minutes, his glancing header from a Sam Stockley cross almost went for a throw in.
The Valiants soon gathered enough momentum to launch an attack and after beating his marker, Chris Birchall picked out Michael Cummins but his strained header fell wide of Aidan Davison's left post.
Nathan Lowndes continued to exploit the weak Colchester left side but failed to get any results when his ball across the face of goal proved too quick for the arriving Billy Paynter after 24 minutes.
All Vale's good work was undone 10 minutes later when calamitous defending allowed Kevin Watson's corner to reach Iwelumo who applied a scrappy touch from four yards to give his side the lead.
Any attempts to equalise before half time seemed a little lacklustre with the best chance being crafted by Paynter, but he could only watch as his curled shot sailed over Davison's angle.
After seeing his direct approach fail, Martin Foyle's decision to add youngster Chris Cornes to the attack seemed to temporarily inject a much-needed sense of urgency.
Birchall's darting run down the left side in the 79th minute raised hopes when he cut back a pass into the path of Lowndes but his low drive from 14 yards never troubled the goalkeeper.
The U's impressive central defensive pairing remained strong to the end, fending off the meek advances that were thrown at them to claim a much-needed away victory.