Danny Invincibile's injury-time volley rescued three points for Kilmarnock when they looked to have to settle for a share of the spoils.
Rhian Dodds was drafted in to replace Killie skipper Gary Locke, and the Canadian's first touch of note set up Dunfermline's opener. Lee Makel floated a free-kick into the penalty area which Dodds failed to deal with, allowing Mark Burchill to swivel and smash the ball into the roof of the net.
Dodds made up for his mistake in the eighth minute when he stabbed Allan Johnston's cute pass past the on-rushing Allan McGregor for a quick equaliser.
The home side grew in confidence and started to play the flowing football which has seen them lose only once in their last 14 games.
Kris Boyd smashed home a second for Killie in the 33rd minute when Garry Hay swung over a tempting cross to give his side a well-deserved lead. Colin Nish and Invincibile both missed good chances to stretch the lead, but the Ayrshire side had to thank goalkeeper Alan Combe for two brilliant saves to deny Burchill before the break. The second effort from a flying header was worth the entrance fee alone.
Killie kept piling on the pressure in the second half but could not find a way through the forest of legs in the penalty area, and they paid the penalty when more slack defending saw Dunfermline draw level in the 67th minute. The defence failed to deal with a standard far post cross, and Derek Young gratefully slammed the ball in off the underside of the bar.
Simon Ford passed up two great chance to win it in the closing 10 minutes for Killie, while Noel Hunt could have completed the theft of all three points but he missed the target when clean through.
Invincibile kept a cool head to latch on to a half-cleared ball in the penalty area in stoppage time to drill a volley low into McGregor's right-hand corner.