Kris Boyd snatched a last minute equaliser for Kilmarnock but it was too little too late as the Ayrshire side's dreams of European football next season all but disappeared.
Although the point keeps Killie in the hunt mathematically they would need to overturn a 12-goal deficit to deny Hearts third spot.
Even a single point had looked doubtful for the visitors after Dunfermline raced into a 2-0 lead in a blistering opening spell.
The first came after just five minutes when top scorer Stevie Crawford flashed a header past Gordon Marshall from a Sean Kilgannon corner.
Six minutes later the Pars had added a second when, after good work down the left from Kilgannon and Chris McGroarty, the latter crossed and Gary Mason sidefooted home from just beyond the penalty spot.
At this stage it looked all over for Kilmarnock and Jason Dair almost added a third after 20 minutes with a well-hit 20-yard drive but it was just wide.
But a freak goal got Kilmarnock back in contention. Peter Canero and Boyd combined in midfield before releasing Gary McDonald on the right after 26 minutes and his deep cross looped over Derek Stillie and in off the post.
Veteran striker Craig Brewster came close just before the interval with only a one-handed Marshall save preventing the goal but it was a different story after the break with Kilmarnock throwing four men in attack.
Sub Andy McLaren, Canero and Paul Di Giacomo all had chances but it looked like poor finishing was going to be their downfall. Their commitment to attack also left them exposed at the back and both Brewster and Crawford should have done better when clear-cut chances came their way late in the game.
But Kilmarnock were not to be denied and Boyd turned Di Giacomo's cross beyond Stillie for a share of the points.