A goal 16 minutes from time by Steven Craig ended our hopes of reaching the Ramsdens Cup Final and saw the Jags reach their first national final since their famous League Cup win over Celtic in 1971.
Ironically Craig who is on loan from Ross County had scored the winning penalty which had put Thistle out the last time they had played in the semi- finals two years ago.
There were three changes to the side which had drawn at Livingston. John Armstrong started a two game ban after his red card while Colin Cameron dropped himself to the bench along with Lewis Coult.
Thomas O’Brien, Ruben Garcia Rey and Kyle Miller all returned to the starting line up.
With just two minutes on the clock McKenzie found Stewart and his 20 yard shot went just wide, then seconds later Stewart showed fine footwork which ended with a neat ball across the six yard box and  Balatoni sliced his clearance over his own bar.
In the 15th minute Bannigan latched on to a loose ball all of 40 yards out and he let fly with a curling effort which Flynn held. Then a minute later Flynn made a treble block firstly from Erskine, who thumped in the rebound only to see the keeper dive to block it before Craig had a go which Flynn again blocked and when the ball flew up Lawless headed over from only eight yards out.
In 27 minutes a long Linton throw was knocked on by O'Brien and Adamson headed over from only eight yards out. As Thistle kept looking for an opening Forbes tested Flynn with a 10 yard header from a well flighted O'Donnell cross with five minutes to go to the break, but on the interval whistle McKenzie's 25 yarder brought out a brilliant finger tip save from Fox.
We started the second-half well and from Linton's long throw Rey's shot from six yards hit a defender and flew out for a corner. Stevenson's delivery was perfect for Adamson's whose header was brilliantly finger-tipped over by Fox.
Cowden were pressing forward eagerly and another Linton throw saw an O'Brien header go over the bar then on the hour mark Stewart made a good run into the heart of the Thistle defence but his 20 yard shot was well held by Fox.
Thistle's first serious attempt of the second period came in the 65th minute when Erskine's 25 yard free-kick curled around the Cowden defensive wall but Flynn saved comfortably.
But with 16 minutes to go Thistle got the crucial goal, Lawless made a break into the Cowden box and he cleverly drew Flynn before setting up Steven Craig who shot low into the net from 10 yards out.
We tried hard to get back into the picture but the closest they came came when Miller got the ball around Fox and Muirhead cleared with the goal gaping.