Two goals in a six minute spell during the second half ended the Cowden youngsters unbeaten run on the Forthbank synthetic surface on Sunday afternoon.
The home side opened the scoring after 31 minutes when a corner from Cooper was cleared but played back into the box by Forbes and Sandy Cunningham was on hand to head home from six yards.
However a minute from the interval Cowden got back into the game when Christie played the ball down the left wing to Johnston who sent over a cross which was fired home by Jack Nicholson.
The Binos restored their lead in 72 minutes when a long range shot from Hamilton crashed off the crossbar and Cunningham slotted home the rebound.
Six minutes later the home side sealed the points when Forbes set up Chris Oglivie who slotted the ball past the diving Barnett from six yards.
With four minutes remaining Cowden almost pulled a goal back when a Christie corner was knocked on by McDonald to Hall whose shot came off the post.