Morton survived a late Cowdenbeath comeback to claim victory at Central Park.
A header and neat conversion by Peter Weatherson put the visitors two up before John Armstrong nodded one back for Cowden on 40 minutes.
Archie Campbell swept home Morton's third and David O'Brien added another with a powerful shot.
Mark Ramsay poked in from close range and Jamie Stevenson stooped to head the hosts' third but it was too little, too late.
Flynn, Brett, Adamson, Linton, Armstrong, McKenzie, Miller, Cameron, O'Brien (Ramsay 55), Stevenson, Coult (Thomas 50). Subs Not Used: Milne, Cowan, Wight.
Armstrong 40, Ramsay 82, Stevenson 90.
Gaston, Dyer, Reid, Mark McLaughlin, Graham, Taggart, Bachirou, Tidser, O'Brien, Weatherson (Wallace 72), Campbell (Stirling 74). Subs Not Used: Naismith, O'Ware, Hutton.
Weatherson 12, 25, Campbell 46, O'Brien 54.