Exeter will face Lincoln in the League Two play-off semi-finals as a 1-0 win over Colchester was enough for them to finish the season in fourth place.
Exeter should have gone ahead in the 13th minute when Liam McAlinden capitalised on some poor defending.
He lofted the ball over the head of goalkeeper Dillon Barnes but opted to set up Robbie Simpson despite having an open goal, with the ball going over his head as the chance went begging.
Simpson had the ball in the net only for the goal to be disallowed for a foul by the Exeter striker, but it was a poor first half of few chances for either side.
On the hour mark, Colchester had a great opportunity to go in front when Pierce Sweeney was adjudged to have fouled Junior Ogedi-Uzokwe in the box, but Sammie Szmodics' penalty was poor and kept out by the feet of Christy Pym.
Dean Moxey fired against the inside of the post for Exeter, who then went in front on 72 minutes when Simpson connected with Sweeney's deep cross to head past Barnes.
Ogedi-Uzokwe's deflected cross had to be palmed behind by Pym, but Colchester rarely threatened as Exeter saw the game out to finish fourth.