The short trip to East End Park saw us go down to the Pars for the second time this season as Jim Jefferies side returned to the top of the table on goal difference from Partick Thistle.
There were three chances from the Raith Rovers game with David Cowan, John Armstrong and Lewis Coult returning while Dean Brett, Ruben Garcia Rey and Kyle Miller dropped to the bench.
In an eventful afternoon that the Central Park faithful will want to forget we lost keeper Thomas Flynn just short of the interval with a head injury while referee Kevin Clancy joined the keeper in the ambulance to the hospital with a calf strain following an accidental clash with Colin Cameron.
As an appeal for an official went out to the crowd the interval lasted for a full 50 minutes with the second period kicking off a 4.35 p.m. after match steward Jock Campbell (61), who normally officiates in the Sunday League got the go ahead to run the line.
The opening 25 minutes saw Dunfermline have the bulk of play but Flynn was not overworked and in nine minutes a good Coult pass was fired over by McKenzie and Stevenson's shot went just over.
In 21 minutes Cameron's pass gave Coult a clear sight of home keeper Gallacher but his finish was weak and the last line saved easily.
In 29 minutes Stewart had control of the ball on the halfway line but he was robbed and Falkingham ran away from the Cowden midfield, who had committed forward, and his pass to Joe Cardle gave the winger a clear opening and he fired the ball past Flynn from just inside the box.
Ninety seconds later Armstrong tried to dribble the ball clear from around the penalty spot and was dispossessed by Barrowman who was fouled by the centre-half but Flynn came to the rescue by saving former Central Parker Husband's penalty kick.
Minutes later Flynn was injured in an accidental clash with Wallace and although he battled on after treatment, he eventually admitted defeat two minutes from the break and Wight replaced him.
The sub 'keeper had plenty of time to think about the task ahead of him as the search for a replacement official dragged on and he was quickly in action after the game restarted and he made good saves from Cardle and Thomson.
On the hour mark Stewart threatened when he took a Cameron pass and his shot landed on the roof of the net and then Stevenson's free-kick was well saved by Gallacher.
Pars sub Kirk brought out a good block from Wight with 20 minutes left with Cowden still in the game but the killer second goal came six minutes later.
A ball slung over from the Pars' right had the Cowden defence in trouble and John Armstrong, in trying to clear, only succeeded in slicing the ball past Wight.
Then in 84 minutes the third arrived. Kirk opened up the Cowdenbeath defence with a fine pass and another sub, Craig Dargo, netted from close in.
Cowden kept probing and with two minutes left Stewart produced a fine save from Gallacher with a 15 yard drive while at the other end Husband saw a shot bounce off the bar.