Stenhousemuir created the better chances in the early stages of the game, but Cowden came closest to scoring on the half-hour when a cross by Iain Mauchlen caught everyone out and struck the post.
The Warriors, however, took the lead in the 38th minute when a Paul McGrillen corner was not cleared properly, and when Colin Cramb played the ball back in Jim Mercer headed home from a tight angle.
The lead was not to last for long, though, as the Stenhousemuir defence struggled to defend a corner and Dougie Hill blasted a shot into the net from the edge of the box with three minutes remaining of the half.
The Fifers took the lead within a minute of the resumption when Liam Buchanan blasted home after an error by Tommy Sinclair cleared the ball into his path.
Cowden became more confident after this, stretching the home defence with Armand One and Buchanan causing umpteen problems, and they had the ball in the net again after 58 minutes but the effort was ruled out for offside.
Buchanan was to be denied another goal in the 81st minute when Chris Fahey made a double save before Mercer cleared another effort off the line, and minutes later Sinclair headed another Buchanan attempt off the line.
In injury-time Stenhousemuir could have stole a share of the points, but Mercer's attempt was well stopped by Cowden's David Hay.
When the final whistle blew, the reaction of the Cowden supporters showed how important a game this was.