A goal two minutes from time by substitute Lewis Hawke, son of Morton legend Warren Hawke, denied us a point against highflying Morton at Cappielow.
There were three changes to the side which had drawn with Airdrie the previous week with Thomas O’Brien, Marc McKenzie and Kyle Miller replacing Joe Mbu, Dean Brett and Colin Cameron.
McKenzie was first to threaten for Cowden in the sixth minute when he found space on the right but shot over.
Morton started to get a grip of possession and they pushed us back without worrying Flynn too much but a Bachirou pass gave Weatherson a chance which he lobbed over.
Coult shot wide before a Tidser cross found Graham whose shot went just wide before a fine Armstrong tackle denied Tidser.
Armstrong was the hero for Cowden again when he raced back to block an O'Brien shot after he had rounded Flynn.
Just before the interval Saparas was replaced by Brett but we were worthy of being level at half-time.
The second period saw Coult link with Stevenson and the midfielder's raging drive went over and then Morton mounted a series of raids which O'Brien and Armstrong, along with Flynn, defied.
Coult was replaced by Stewart but he had been on only ten minutes when he had to go off with Navas entering the fray.
It meant that the we were lacking firepower and were forced to play a containing game which worked pretty well as Morton were reduced to long range efforts to try and break the deadlock.
The game was drifting towards a draw when, with just two minutes left, Graham's cross found Lewis Hawke, who had just come on, and the teenager had time to fire the ball out of Flynn's reach.
There was little time for Cowden to respond and the result was a real blow after all the effort that we had put into the game.