A goal in each half from Kevin O’Hara meant that John McGlynn’s side missed out on he opportunity to move level on points with fourth-placed Partick Thistle as they try to finish in a play-off position.
With only four games left, Rovers are running out of time and how damaging this loss could be remains to be seen.
Whatever the outcome, it was a disappointing performance and a real come down from the weekend win over Queen of the South.
Raith made three changes to the SPFL Trust Trophy winning line-up, with LIam Dick, Ethan Ross and Ethon Varian all dropping to the bench, in their places came Kyle Benedictus - back from suspension - Dario Zanatta and Brad Spencer, making his first appearance since December 2 after recovering from a broken leg.
Heavy rain fell in the lead up to kick off and combined with a swirling wind, conditions were far from ideal for the last Fife derby of the season.
The first 15 minutes saw the two evenly matched, a dangerous ball across the face of the visitors’ goal from Pars’ Matthew Todd was the closest either came to breaking the deadlock.
The home side had the first proper effort on goal with a shot from Steven Lawless six minutes later, but Jamie MacDonald was untroubled in the Rovers’ goal as it went wide.
In truth it was a dull opening half hour in keeping with the three previous meetings between the sides so far this season, so when the deadlock was broken shortly after it was no surprise that it came from a mistake, rather than a moment of quality.
In the 33rd minute Spencer dithered at the edge of his own box and was dispossessed by Liam Polworth.
O’Hara pounced on the loose ball and left one-on-one with MacDonald, made no mistake.
Just before half time, the home side passed up a glorious chance to double their lead.
They broke from midfield and Dom Thomas played the ball square to Lawless but with time and only MacDonald to beat, he blazed his effort well over the target.
The break duly arrived with Raith lucky still to be just a goal behind and with an improvement badly needed for the second 45.
Substitute Ross emerged to replace Zanatta as Rovers looked to get back into the game but after just a minute of the restart Dunfermline went close again.
Centre half Efe Ambrose was just inches away from knocking in a Thomas free kick after being left unmarked in the Raith six yard box.
The hosts were well and truly on top in the early stages and looked dangerous every time they went forward with a second goal, but to their credit Rovers weathered the storm and played their way back into the match.
Spencer was replaced with striker Varian as Rovers switched to a front two and immediately had their first proper attempt on goal - Sunday’s two-goal hero Matej Polatnik nodding over after Ambrose had headed a cross from Sam Stanton backwards inside his own box.
Varian just missed getting on the end of a low cross from Reghan Tumilty before Coll Donaldson headed wide from a corner at the other end.
With 15 minutes to go the Pars passed up yet another great chance to score, this time it was O’Hara left with just MacDonald between him and the net but hit his effort weakly against the Raith goalkeeper.
However just three minutes later he would make amends with his and Dunfermline’s second goal, knocking in after Lawless’ corner to the Raith front post had caused a scramble.
With three minutes to go Raith had their solitary effort on target, a weak header from Varian which trundled towards Pars keeper Jakub Stolarcyk.
The match ended in defeat for Raith and meant that they have failed to beat their fiercest rivals in all four meetings this season – a side which has spent the vast majority of the 2021/22 campaign in the bottom two.