Jamie Cureton had given the Grecians a half-time lead but two goals in the final three minutes from Ian Henderson and Bobby Grant did the damage for Dale.
Defeat for Exeter sees them clinging on to a play-off place after a poor Easter in which they lost twice.
"It was terribly disappointing because it happened so late in the game," Tisdale said. "With five minutes to go we were leading 1-0 and you just hope you can hang on considering how poor we were.
"You hope you can hang on and to be at that point and then concede so late, and then an injury-time winner, is very disappointing.
"We have lost the game but we are still in the play-off zone and we still have six games to go, so I can spin positives from it, but it feels so disappointing because of how poor we were as a team.
"I have not seen one of my teams play so poorly for a long, long time and we struggled to put passes together or play any meaningful forward play at all.
"I used words on Saturday like fractured and not being cohesive and there being no fluidity to our play, and it needs experience to tidy the play and keep things together and it was the same again here."