Thistle contested their first cup final in five years but, despite dominating large spells of the match, failed to bring the Glenfield Autocentre Cup back to Balmullo.
Despite edging the play it was the Perthshire side that opened the scoring when Bell was adjudged to have pushed McNiven in the box resulting in a penalty which was converted by Moffat.
Thistle came close to an immediate response when Gray went close with a speculative effort that had Doig scrambling.
Harris came close on the hour after Whatmore cut the ball back as Thistle turned the screw but with 84 minutes gone they finally drew level when a surging run from Allan saw Nicolson take possession. The youngster turned back inside before delivering a perfectly weighted cross which Harris headed into the roof of the net past the helpless keeper.
Thistle continued to push for the winner however time was against them and the match went to penalties. Unfortunately Harris and Mackie missed the opening two penalties and with Bridge of Earn converting every spot kick they took the honours and their first trophy since switching to the Kingdom of Fife Association.
LM Joinery Man of the Match – Ryan Gray
Thistle: Wortley, Carson, Leadbetter (Finlay 66), Bell, Whatmore, Gray, Mackie, Fox, Allan, Barnes (Nicolson 73), Harris.
Subs: Anderson, Walker, McColm.
On Thistle play host to Markinch in the league with a 2pm kick off at Balmullo then on Tuesday end the 2021-22 season away to Burntisland United with a 6.45pm kick off.