It was the midfielder's second goal of the game and took him into double figures for the season, latching on to a cross from substitute Chris Beardsley with an acrobatic effort from 12 yards.
Exeter had taken a 20th-minute lead in fortuitous circumstances. David Wheeler controlled the ball at the far post and, when Lee Brown challenged, it span off the Rovers defender and looped over goalkeeper Steve Mildenhall for an own goal.
But within seconds Rovers were level as Eliot Richards was tripped by Danny Butterfield inside the penalty area and O'Toole converted the spot-kick with a low right-footed shot into the bottom corner.
Richards had earlier been guilty of one of the misses of the season, somehow shooting wide when Ellis Harrison's run and cross left him in front of an unguarded net.
But OToole spared his blushes late on and Exeter could count themselves unlucky on the balance of play.