Substitute Willie McLaren scored within two minutes of his introduction at East End Park to ensure the Diamonds finished a disappointing season on a positive note.
The visitors opened the scoring inside the first minute of the second half through Liam Coogans and although Ryan Thomson levelled on 58 minutes, Airdrie mustered a quick reply through McLaren to clinch their first league win since January.
Dunfermline must now prepare for a promotion/relegation play-off with Forfar, who finished fourth in Division Two.
The Pars suffered an early setback when teenage striker Allan Smith was stretchered off inside the opening minutes, and it took a timely intervention from defender Callum Morris to deny Liam Watt.
Dunfermline goalkeeper Michal Hrivnak made a fine save from Jamie Bain on 18 minutes, while at the other end Thomson crashed a shot off the underside of the crossbar.
Ryan Wallace fluffed a great chance after he was teed up by Thomson and that missed proved costly when Coogans netted within a minute of the restart.
Wallace missed another opportunity on 56 minutes but Dunfermline were soon level, Thomson bursting through the middle and rifling home.
But Dunfermline weren't on level terms for long, McLaren unleashing a 30-yard strike past Hrivnak on 62 minutes for his third goal of the season.
Thomson and Alex Whittle both spurned good chances as Dunfermline pushed for a late equaliser, but Airdrie hung on for a rare win.