Saints went ahead after just ten minutes, when some comic defending gave John Sutton the chance to curl the ball into the bottom corner from the edge of the box.
Dunfermline equalised just a few passes after the break, Darren Young placing a shot into the net that gave Tony Bullock no chance.
Dunfermline seemed to have improved after the break and a mistake from David van Zanten allowed Stevie Crawford to score the winner just 15 minutes from time with another shot that Bullock had no chance of getting to.
Not good for Saints, as this was a game many thought we'd take at least a point from. Next week it's Hibs at Love Street, and they lost to Falkirk today.