Despite the Accies having much of the first-half possession, it was the visitors who made the best chances in front of goal, with Mark Roberts coming closest with a header over from close range after 17 minutes.
After 36 minutes Thistle's Craig Sives headed into the side net from a Scott McCulloch cross. The goal was only delayed a further minute. Derek Young collected a pass from Adam Strachan before slipping his marker and coolly shooting past Ramond Jellema.
Thistle started the second half the same way they finished the first, camped in the Accies half. Roberts was once again the man who came closest as his shot was saved at the near post.
To change the flow of the game Accies made two changes, and this seemed to work. They gained a deserved equaliser after 64 minutes. A Derek Fleming corner was swung into the six-yard box, and inexplicably Billy Gibson palmed the ball away.
Tony Stevenson stepped up to take the spot-kick and smashed the ball high into the roof of the net, leaving Jonathan Tuffey no chance.
Thistle also made two changes, and this produced immediate results when they combined to score the winner with two minutes left. A Pat Keogh flick found Graham Gibson, who shot past the hesitant Jellema