A goal near the end of the first half proved to be the clincher that took the Blue Toon to the top of the table.
Peterhead made just the one change to the starting line up that had beaten Stirling Albion three days earlier, Jack Leitch starting ahead of the benched Willie Gibson.
It was the visitors who started the brighter, a 2nd minute corner kick from Gary Fraser headed over from close in by centre half Robbie Deas.
The Blue Toon response was a left wing cross by Paddy Boyle just missed by Rory McAllister who appeared to be nudged away from the flight of the ball.
The home side proceeded to dominate as has been the norm so often this season and a bicycle kick from centre back Mick Dunlop on the quarter hour went narrowly past the right hand post.
A couple of minutes later it should have be one nil to Peterhead, a well struck volley 25 yards out by Scott Brown went into the turf before kicking up and heading towards the roof of the net until Aaron Lennox made a fine save tipping the rising shot over the crossbar.
A mazy run by McAllister taking him past several bamboozled Blue Brazil defenders concluded without an end product then Shane Sutherland blasted over when well placed as possession failed to be turned into an all important goal.
Eight minutes before half time Peterhead had another half chance, Jamie Stevenson touching a free kick to McAllister but his snap shot was well held first time by Lennox.
Their persistence eventually paid off with an opener after 43 minutes. McAllister managed to keep a loose ball in play at the back post and Brown pounced from six yard to poke his shot home for a scrappy but vital goal.
The Blue Toon were fast out of the blocks after half time and McAllister failed to hit the target with an early header before Sutherland couldn't quite manage a touch on a squared ball across the edge of the six yard box.
Cowdenbeath responded with a neat passing attack with play switched from right to left, Fraser Mullen crossing and Harvey Swann earning a corner in a rare attacking move.
Normal service was soon resumed though and home defender Jason Brown scooped a shot over as they sought the comfort of a second goal.
A snap shot wide by centre half Deas kept the Peterhead defence on their toes on the hour but at the other end a sweeping move from Brown to Stevenson squared to sub Derek Lyle produced a goalbound shot unbelievably stopped on the line by the prostrate body of Leitch.
Another chance for the Blue Brazil kept the home defence on their toes, sub Matthew Henley dragging a low shot from the right side if the area wide of the far post.
Ryan Dow inexplicably sent a point blank header wide for Peterhead as the elusive second goal simply wouldn’t materialise. Despite 26 efforts on goal, a win by the slimmest of margins was enough to take Peterhead to the summit in Division Two.