Aaron Wilbraham sent a low shot wide inside 13 minutes after Mark Randall’s defence-splitting pass had sent him through, but Colchester took the lead five minutes later.
Marc Tierney’s long throw into the area was not properly dealt with by keeper Willy Gueret, who was under pressure from Clive Platt, which allowed Kevin Lisbie to lash the ball home for his 11th goal of the season.
Colchester should have doubled their lead eight minutes into the second half after substitute Jude Stirling was adjudged to have fouled Lisbie in the area and was sent off, but Gueret saved the striker’s penalty.
However Prutton, on loan from Leeds, doubled Colchester’s lead less than three minutes after coming on as a substitute, lashing a rasping 25-yard shot into the top corner.
Substitute Sam Baldock hit a post for Dons late on but Colchester were worthy winners.