Paul Hampshire's first goal for the club sealed a bruising derby win for Jim Moffat's East Fife side.
East Fife went straight for their rivals and opened the scoring after 10 minutes with Cowden looking for an offside flag.
Marco Pelosi launched a ball over the top and Hampshire killed it before turning and firing past David Hay.
John Martin then shot narrowly wide before Robert Downs came close for the visitors when he nodded past the post after 13 minutes.
Cowden almost grabbed an equaliser 10 minutes later with a fierce Kevin McBride half-volley from the edge of the box, but John Dodds beat it away.
Dougie Hill then saved a certain goal before the break when he threw himself in front of a John Bradford close-range shot.
Hampshire and Gavin Beith were just off target from distance, but Cowden came much closer with Iain Mauchlen's shot which just crept over the bar.
Cowdenbeath trialist Marcus Paatelainen, brother of boss Mixu, almost embarrassed Dodds with a strike which the keeper nearly fumbled into the net after 52 minutes.
Cowdenbeath kept up the pressure and brought on all their substitutes to try and find a leveller. Liam Buchanan had the crowd on their feet after 72 minutes when he managed to get his head to a Marc Millar free-kick, but his effort lacked power.
The visitors couldn't find a way past the stubborn Fife defence, and East Fife substitute Johnny Mitchell should have made the score more emphatic with a late drive which was well saved.