The three points lift Cowdenbeath back to the top of the third division table following Berwick's victory against previous leaders Stenhousemuir.
The Blue Brazil's top scorer Liam Buchanan should have scored in the opening stages but saw his effort blocked by Albion keeper Gary McGlynn.
The visitors took a shock lead four minutes before the interval when poor defending allowed Scott Chaplain to net.
Iain Mauchlen and David McKenna wasted two excellent chances to equalise before loanee David McKenna scored two goals in three minutes to bring his recent tally to nine goals in 14 games.
Albion tried in vain for a late equaliser as recalled Cowden keeper Andy Carlin kept them at bay.