The Blue Brazil took the honours from the first derby of the season after coming out on top in a thrilling game at Central Park.
Ryan Wallace opened the scoring for the visitors with a rasping half volley after only 3 minutes but Greg Stewart (17) evened things up after rounding the keeper to score his first goal of the season.
Cowden took the lead for the first time just after the interval when Matthew Park (52) put through his own goal from a Scott Linton cross only for David Muir to level the scores 10 minutes later.
Either side could have won this end-to-end game but skipper Jon Robertson claimed the winner with 14 minutes to go after his deflected free-kick deceived Mark Ridgers.
The home side had a number of chances to finish the game before a late East Fife free-kick came back off the bark and Yossi Bejaoui made a last gasp save to deny John Robertson's side.
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