Steve Crawford put Dunfermline in the driving seat at Love Street.
He opened the scoring after eight minutes with a superb strike to stun St Mirren.
There seemed little danger when Crawford latched on to a ball from Justin Skinner but his turn and shot from the edge of the area were straight out of the top drawer.
The goal stunned Saints, who went into the match rooted to the foot of the Premier League table.
They carved out the first opening of the game when Sergei Baltacha floated in a cross from the left but Andrius Skerla was able to prevent Mark Yardley getting good contact.
Skerla's return after injury was a boost for Dunfermline, aiming to cement a place in the top six.
Crawford's goal raised their spirits and Jason Dair sent a shot over the top after Baltacha had lost possession.
St Mirren went into the match on the back of a victory against St Johnstone but Crawford's goal once again exposed their fragile confidence.
Dunfermline were looking assured and not content just to sit on their lead.
The Saints showed no lack of commitment in the early stages but Graham Fenton was over-zealous in the 25th minute.
He picked up the first yellow card of the game for a crude challenge onMichel Doesburg, which left him needing treatment.
The home supporters, who last year celebrated promotion, were becoming increasingly frustrated.
Dunfermline again pressed forward in the 35th minute and left Saints stunned with their speed of movement.
Scott Thomson played a delightful one-two with Tomas Danilevicius, on loan from Arsenal, but keeper Ludovic Roy made a good block.
Lithuanian defender Skerla, such an influential figure for Dunfermline, linked up with the attack two minutes before the break.
However his shot was deflected to safety with Saints forced to back pedal.
Both sides came up from the first division in the summer but in the first half Dunfermline looked faster and sharper.