Dundee started on the attack and were one up with just 89 seconds on the clock.
A long defensive clearance was flicked on by Steve Lovell to Steve Milne, who stood 10 yards from goal and he lifted the ball over Thistle keeper James Langfield and into the back of the net.
Two minutes later Nacho Novo almost made it two when he rounded the keeper and fired his shot goalwards but Grant Murray raced back and booted the ball clear a yard from goal.
The visitors drew level with 14 minutes gone when Jamie Mitchell raced clear down the right and crossed to Andy Thomson who made no mistake heading high past Julian Speroni from inside the six yard box.
David Rowson had a good left foot drive from 30 yards which went inches over 10 minutes before half time.
Julian Speroni did well to turn a close range Andy Thomson header around the post with 30 minutes played.
A snap shot by ex Dundee favourite James Grady was well saved by Speroni early in the second half.
Midway through the second half Garry Brady's goal bound effort was cleared for a corner and from the kick Lee Mair fired high over the bar. Dundee grabbed an unlikely winner with 90 minutes on the clock.
A free kick by Gary Brady was floated into the box and when Sebastian Kneissl and keeper James Langfield both went for the ball it fell nicely for Novo to fire the ball into the back of the net from close range to secure Dundee all three points.