In a game postponed due to fog on December 10, James Fowler's deflected shot after 21 minutes put Killie ahead as the visitors sought to avenge the 3-0 loss to the Pars on January 21 and return to the top half of the table.
Andy Kirk equalised after 44 minutes, and although Dunfermline's search for a first home victory of the season goes on, the Pars moved level on points with Hibernian at the foot of the SPL standings, while Killie moved seventh.
Dunfermline made five changes from the side which lost to Aberdeen on January 28, with on-loan Rangers midfielder Kyle Hutton and former Ger Jordan McMillan making their debuts and the fifth enforced after goalkeeper Iain Turner suffered a back problem in the warm-up, with Chris Smith a late replacement.
Kirk fired off-target after 14 minutes before a good cross from his strike partner Liam Buchanan evaded everyone.
Killie then took the lead after Dunfermline failed to clear Lewis Toshney's cross from the right and the ball fell for midfielder Fowler to net a deflected shot down the centre of the goal.
Dean Shiels had an effort saved before almost setting up a chance for Paul Heffernan, only for Alex Keddie to get in front of the Killie striker and Smith to collect.
Smith saved a Shiels shot on the turn before Dunfermline equalised one minute before the interval.
David Graham burst through the centre of the field and prodded the ball forward to Kirk, who beat the offside trap.
With Cammy Bell advancing from his line, Kirk shot early into the bottom corner.
Buchanan shot across goal but wide early in the second half before Dunfermline were almost undone by their own defending.
A Kirk pass-back fell for Heffernan, who prodded goalwards, but Smith managed to spread himself and save well.
Having shown his strong side, Smith, who has made a number of gaffes this season, then made manager Jim McIntyre anxious.
The goalkeeper ballooned a clearance kick high in the air and was fortunate Paddy Boyle was present to clear.
Smith then saved low to his right from Garry Hay and substitute Dieter van Tornhout's header from Heffernan's cross bounced off Kevin Rutkiewicz and out for a corner as the visitors continued to look the more likely to take the lead.
Toshney was bundled over on the edge of the area, but nothing was given and Van Tornhout's heavy touch saw Kirk go clear at the other end, only to flash a shot wide.
Hutton was booked for bringing down Shiels after being beaten by the Killie playmaker, presenting the visitors with a free-kick from a promising position.
Hay hit the resulting set-piece on target and Smith managed to palm the ball around the post before being relieved to see it go out after flapping at the resulting corner.
Manuel Pascali's header from a further corner was cleared off the line by Kerr before Killie scrambled clear a set-piece at the other end, with Pars substitute Martin Hardie's shot hitting a defender as the match finished drawn.