Dundee took all three points with two late goals in a match neither side deserved to win.
The tension surrounding this relegation struggle seemed to affect both sides, particularly in the opening stages, with no clear chances until the 24th minute when Derek Fleming shot wide of Julian Speroni's goal.
The same player had the next chance on 29 minutes when his 22-yard free-kick went the wrong side of Speroni's far post.
Thistle's first shot on target produced a goal when David Rowson connected with a poor defensive header to volley home from 20 yards.
Although enjoying the majority of possession it was fully 43 minutes before Dundee troubled Thistle's new keeper Jamie Langfield, when Garry Brady's shot was well saved.
The second half continued much the same as the first, however James Grady almost extended Thistle's lead on 50 minutes, but his chip just went the wrong side of Speroni's left hand post.
Dundee's Nacho Novo was perhaps fortunate a minute later when he appeared to stamp on Rowson, but the officials missed the incident.
Thistle appeared to be happy defending their slender advantage as the Dark Blues continued to press for the equaliser.
Both sides had further chances with Steven Robb and Lee Wilkie coming close for Dundee and Ken Milne and Grady coming closest for Thistle.
The visitors equalised in controversial circumstances on 85 minutes when Novo, who appeared to be in an offside position, was able to connect with Milne's low cross to tap home from two yards out.
Thistle were now trying to hold out and claim a point which would have kept them within touching distance of Dundee at the foot of the table, but the Dark Blues scored the winner on 89 minutes with a spectacular volley from captain Barry Smith.
He connected with a punch from Langfield, who had no chance with the rocket of a shot.
After this result Thistle now lie 12 points behind Dundee and even at this early stage look certainties for relegation.