Thistle gave their fans a belated Christmas present with only their second league victory of the season.
Dunfermline created the first chance after only 40 seconds when Scott Thomson's free-kick beat everyone in the box and went just the wrong side of Kenny Arthur's far post.
Thistle's first chance fell to Andy Thomson after three minutes but Derek Stillie rushed from his line to block the shot.
Following this early spell, chances were few and far between and it was fully 17 minutes before Dunfermline earned the first corner of the match but this came to nothing.
Neither side were able to dominate play with a lot of passes going astray much to the disappointment of both sets of fans.
Thistle took the lead against the run of play when a Derek Fleming cross found Thomson unmarked and he headed home from eight yards past Stillie into the far corner of the net.
Dunfermline made two changes at half time and Gary Dempsey almost made an immediate impression but his 20-yard shot was blocked for a corner.
Thistle's first corner came in the 53rd minute and Dunfermline appeared to have cleared the danger. However, the ball fell to James Grady and his cross was about to be headed home by Jamie Mitchell when Thomson bundled him to the ground and was sent off for his troubles. Grady made no mistake from the resulting penalty.
Ten-man Dunfermline did manage to pull one back on 59 minutes when Craig Brewster volleyed home from 12 yards giving Arthur no chance.
Chances then fell to both sides with Thomson missing a succession of chances that would have made the game safe for Thistle and Steve Crawford heading wide from close range for the visitors.
Dunfermline continued to press for the equaliser and they paid the price for this when Thistle broke clear in the 89th minute and Andy Ross made sure of all three points when he fired home from Stephane Bonnes' cutback.
Thistle scored again in the last minute from a similar position, this time Grady connecting with Emanuel Panther's cross.
Thistle will be delighted with these points but Dunfermline will be equally disappointed as they missed their chance to go third in the league.