Craig Lindfield was the Accrington hero as his winner secured a third win in four games and boosted Stanley's battle against the drop.
Liverpool loanee Lindfield fired home Chris Turner's cross on 64 minutes to dent Exeter's promotion hopes.
Exeter led on five minutes when a Craig McAllister flick set up Adam Stansfield for his 10th goal of the campaign.
But Stanley battled back and a Peter Cavanagh corner found John Miles who curled a shot into the roof of the net.
Exeter City manager Paul Tisdale told BBC Radio Devon:
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"I'm disappointed, but it's not over, we've got lots of football to be played yet.
"I thought we were fabulous in the first 15 minutes, possibly the best we've started all season.
"It looked like we could win by four or five by the way we started."
Accrington Stanley: Arthur, Cavanagh, Charnock, Edwards, Williams, Procter, Ryan, Turner, Miles, Lindfield, Symes. Subs not used: Murdock, John Mullin, Grant, Hibbert, Kay.
Booked: Lindfield.
Exeter: Jones, Seaborne, Edwards, Archibald-Henville, Moxey, Sercombe, Stewart, Russell, Gill, Stansfield (Saunders 72), McAllister (Fleetwood 62). Subs not used: Marriott, Tully, Cozic.
Att: 1,169
Referee: Karl Evans (Greater Manchester).
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