A last gasp equaliser from Simon Mensing denied us a derby win after twice leading by a two goal margin.
There were two changes to the starting line up after the narrow defeat from Partick Thistle with David Cowan and Scott Linton side lined with injuries Dean Brett and Colin Cameron returned to the side.
It took just four minutes for us to open the scoring Stewart's persistence got him into the Rovers box and his low shot was blocked by McGurn but the ball fell kindly for Kyle Miller who forced the ball over the line from six yards out.
Rovers responded and Graham worked a good position for himself in the heart of the Cowden box but Mbu came to the rescue with a fine tackle.
The Blue Brazil added number two in 23 minutes when Rovers gave away a free-kick 30 yards out through Hill's challenge. Jamie Stevenson stepped up to fire a lovely low shot wide of McGurn.
Rovers were stunned by this blow but in 35 minutes they got one back when Flynn grabbed the ball after it had been played by Rey. It seemed a harsh decision as the ball bounced off the defender.
An indirect free-kick was awarded eight yards out and Brian took Walker's pass to shoot low into the net from only yards out.
The equaliser arrived sixty seconds from the break. Hamill's corner was perfect for Greig Spence whose header flew over Flynn from close in.
Play became bogged down in midfield for a spell in the second-half but we threatened in 67 minutes when  Adamson latched on to Stewart's pass but fired his 18 yarder too high. Some hesitant defending by Rovers with 20 minutes left almost let Stewart through but Mensing managed to knock the ball inches past his own left hand post for a corner.
However, in 78 minutes Cowden got number three when a left wing cross was brilliantly headed home by super sub Lewis Coult and then two minutes later the big front man grabbed his side's fourth when the Rovers defence got in a right fankle, and while his first shot was blocked by McGurn, he followed up to slot the ball home from 10 yards out.
But Raith were not beaten yet and substitute Pat Clarke grabbed a third for them after Graham again foxed the home defence and then in the third minute of time added on Simon Mensing’s effort beat Flynn for the leveller to leave the home players and fans deflated.