The Cod Army had been hoping for three points to reignite their play-off charge, but Stewart's late header ensured it is now four games without a win in League Two.
The visitors controlled the opening exchanges but Wycombe had the first chance when Sam Wood met Josh Scowen's corner in the eighth minute but he scuffed his shot wide.
And they came close again in the 20th minute when Wycombe player-manager Ainsworth had a long-range effort tipped wide by Scott Davies.
Gareth Evans, starting for Fleetwood for the first time in three weeks, broke through on goal with ten minutes left in the half but Jordan Archer came out and blocked.
The sides continued to trade chances, with Junior Brown going close to breaking the deadlock when he headed Jon Parkin's cross towards goal but Archer's diving save denied him.
David Ball replaced injured Steven Gillespie in the 43rd minute and almost had an immediate impact for Fleetwood but he volleyed just over from Evans' cross.
Top-scorer Brown flashed wide from a tight angle after driving into the area in the 58th minute as Fleetwood started to turn the screw.
Ainsworth, who came off injured, urged his side forward from the sidelines but both teams failed to create any clear-cut chances.
But in the final minute Stewart had an effort cleared off the line by Jon Parkin and from the resulting corner he scored his first goal for the club to break the deadlock.
And 17-year-old Junior Morias, on as a substitute, could have sealed the win but he rolled his shot just wide when through on goal.