Mark Stewart belied an untidy first half with the neatest finish after 29 minutes when he pursued a pass from Ryan Conroy before hoisting the ball high into the net.
Raith took the game out of Cowdenbeath's grasp after half-time. It was no surprise when Lewis Vaughan gave Raith their second goal with 20 minutes left - heading Stewart's delivery back across goal and beyond home goalkeeper Thomas Flynn.
Conroy extended Raith's lead with a fiercely-struck free-kick from 25 yards which left Flynn with no chance.
Lewis Milne got a late consolation for Cowdenbeath with an assured strike from outside the penalty area.
Dumbarton claimed their first points of the season by winning a tight match with Livingston 1-0 at home.
It was a game that ebbed and flowed but it was left to Chris Kane to provide the decisive moment, a header late in the game.
Gary Glen had an early chance for Livingston, but, left unguarded in the penalty area, he headed off target.
Kyle Jacobs almost broke the deadlock for Livingston just after the break but his header hit the crossbar.
An earlier Kane effort needed Kyle Jacobs to head it off the line, but he was not to be denied.