A last-minute James Craigen penalty gave Rovers a dramatic win and ended Morton’s six-game unbeaten run.
While it was the home side who dominated the early exchanges, Raith were on top throughout the second half and just about deserved the win which takes them back into the promotion play-off places.
Rovers made a bright start but Morton were first to threaten when Ross Forbes was upended by Scott Robertson 30 yards from goal and Joe McKee curled the free-kick round the defensive wall and narrowly wide of target.
Bobby Barr then embarked on a probing run down the left flank before feeding Alex Samuel whose shot tested Kevin Cuthbert.
Play began to become bogged down in midfield but the match sprang to life when Morton grabbed the lead with a well-worked goal on 23 minutes.
McKee fed Denny Johnstone who burst into the box and teeing up Forbes whose first-time effort was parried by Cuthbert. However, the rebound fell for Samuel who bundled the ball home despite the presence of two Raith defenders on the goal-line.
Rovers responded with a snapshot from Ross Callachan which gave Grant Adam his first serious action of the evening though the keeper was well placed to make the save.
Morton might have doubled their lead when Samuel turned his marker and sent an inviting ball over the face of goal but Johnstone just failed to connect.
The home side went even closer when McKee’s corner was met by a firm Thomas O’Ware header which was parried by Cuthbert, the keeper recovering to make a second save when the rebound cannoned off defender Lewis Toshney.
At the other end Adam, under intense pressure from Jon Daly, took two efforts to gather Mark Stewart’s swirling cross. The Cappielow keeper then dived to hold Stewart’s angled shot as Raith rallied.
Ray McKinnon’s men got their reward immediately after the restart when Stewart slipped a pass to Callachan whose 20 yard shot took a wicked deflection to leave Adam helpless.
For the first time in the match Raith looked clearly on top and Ryan McCord squandered a good chance when he fired over from the edge if the box.
The Kirkcaldy side thought they should have had a penalty when Stewart’s cross struck Connor Pepper on an outstretched arm. However, referee John McKendrick gave the Morton man the benefit of the doubt.
Stewart then saw his shot deflected inches over as Rovers pushed for a winner, which they got at the death when Mark Russell fouled Mitch Megginson in the box and Craigen calmly slotted the penalty.
Morton: Adam, Pepper, Kilday, Gasparotto, Russell, Forbes, O’Ware, McKee (Miller 75), Barr (Quitongo 86), Johnstone, Samuel (McCluskey 83). Unused Subs: Lamie, Scullion, Orr, Gaston.
Raith Rovers: Cuthbert, Toshney (Bates 35), Davidson, Benedictus, McKeown, Callachan, McCord (Matthew 68), Robertson, Craigen, Stewart (Megginson 79), Daly. Unused Subs: Petrie, Wighton, Ellis, Law.
Referee: J McKendrick.