The Sky Blues, aiming for their highest finish since dropping out of the Premiership, took the lead in the eighth minute after a bright start.
Leading scorer Gary McSheffrey found space down the left flank and delivered a telling cross. Glenn Loovens tried to clear but only managed to mis-kick and that allowed Stern John to pounce and ram the ball in past Neil Alexander.
Coventry had certainly begun the game with more pace and purpose and got considerable joy down the left flank with Marcus Hall and McSheffrey both doing well.
But Dave Jones' men did start to find their feet and should have done better just four minutes after going behind. Joe Ledley got forward down the left and sent over a good cross, but Guylain Ndumbu-Nsungu failed to make contact.
But the Welshman did get level in the 21st minute when an error from Richard Shaw - playing his last game for Coventry - allowed Ndumbu-Nsungu to tee up Steve Thompson, who scored from close range.
Both sides had chance to add a second, but the finishing was distinctly end-of-season. McSheffrey went closest for Coventry, while Ndumbu-Nsungu shot wide from long distance.
Micky Adams was clearly not going to let the chance of victory go lightly and he made a couple of early substitutions.
But it was the visitors who looked more likely and only the woodwork saved Coventry when Jason Koumas went on a darting run and let fly with a curling shot which had keeper Marton Fulop beaten.
But just seven minutes later they found themselves behind as Coventry sliced them apart with a very good move.
Michael Doyle - who has just signed a two year contract - hit a slide-rule pass between two players allowing Dele Adebola to run into the area and score past Alexander with his left foot.
Young Andrew Whing set up what looked a certain goal for veteran Don Hutchison when he delivered a low, driven cross in the 72nd minute, but the former Everton and Liverpool man somehow fire wide.
Whing got it right again in the final minute when he centred for Dennis Wise to nod home his sixth goal of the season.