The home side started well and looked more likely to score early on when trialist Steve Mallon had a good effort saved by William McCulloch in the Stenhousemuir goal after just five minutes.
However, the visitors took the lead with their first real attack in the 18th minute. A great breakaway found Paul McGrillen on the left, but his low shot looked as if it would be easily saved by Andrew Carlin.
But Carlin could only knock the ball six yards out into the path of the incoming David McInally who blasted it into the net.
Stenhousemuir looked the more composed for the rest of the half, although John McKeown had a header cleared off the goal line by Tommy Sinclair during a rare home attack.
The visitors almost put the game beyond doubt after the restart when McGrillen smashed a shot off the post, but Cowdenbeath never looked like drawing level, despite creating a number of half chances.
Stenhousemuir keeper William McCulloch had to look lively to save an Innes Ritchie header but, at the other end, a shot from McInally hit the top of the crossbar.
The Warriors finally sealed the points five minutes from time when McGrillen's cross from the right was glanced into his own net by McKeown.