In an absorbing game played in occasionally atrocious conditions, Killie striker Conor Sammon missed a sitter just after the break before Danny Invincibile gave the home side a 77th-minute lead, which at that point they had deserved.
However, the visitors fought back and six minutes from the end Killie goalkeeper Mark Brown fumbled a Charlie Mulgrew free-kick down at his left-hand post and McDonald, a former Rugby Park midfielder, gleefully knocked the ball into the empty net from close range.
Killie boss Jim Jefferies will point to a couple of chances to have tied the game up - not least Sammon's glaring miss from seven yards after he had been set up by David Fernandez - but the draw was arguably a fair result.
The blustery conditions promised a difficult afternoon for both sets of players but in the eighth minute Dons midfielder Peter Pawlett came close when, from 12 yards out, he headed Stuart Duff's deep cross just past the far post.
Seconds later, Killie skipper Garry Hay fired the ball into the Dons box, forcing goalkeeper Jamie Langfield to make a fine save before captain Mark Kerr ushered the rebound to safety.
In the 18th minute Langfield looked less impressive when he misjudged Jamie Hamill's long, hopeful punt into his box following a cleared corner.
The Aberdeen goalkeeper allowed Killie defender Steven Old to beat him to the aerial challenge 10 yards out and was relieved to see the ball hit the top of the crossbar before going over.
Then it was Aberdeen's turn to hit woodwork when Brown tipped a close-range shot from Michael Paton on to the crossbar and over, following a terrific inswinging free-kick from Mulgrew which had the Rugby Park defence in all sorts of trouble.
The game was warming up at last and moments later, as the home side broke, Sammon drove an angled shot straight at Langfield, who blocked with his legs.
The second half resumed in awkward fashion but in the 49th minute, after Mulgrew had been penalised for a foul on Sammon 30 yards from goal, Langfield had to throw himself to his left to keep Hay's curling free-kick from creeping in at the near post.
Neither side were keeping possession for any length of time but in the 51st minute Sammon missed a great chance to grab the opener.
Fernandez took a pass from Hamill and raced into the box before knocking the ball inside to the unmarked Irishman, who was barely seven yards out.
However, with the Killie fans on their feet ready to celebrate the opener, Sammon mis-hit his shot and the ball hit Langfield before bouncing past for a corner, which the Dons defended.
The heavens opened again as the Pittodrie side rallied and moments later, a mistake by Old at the edge of his own box was almost punished by Pawlett but his shot lacked the power to trouble Brown.
Sammon almost made up for his earlier error when he curled a shot from the edge of the box past Langfield but also past the far post.
In the 76th minute Allan Russell replaced Fernandez to make his first appearance of the season and a minute later he set up the opener for Invincibile.
As Killie broke against a threadbare Dons defence, Russell rolled the ball to the Australian who drove powerfully under Langfield from just inside the box.
Moments later, as Killie relaxed, Brown made a fine save from Chris Maguire's angled shot before Sammon missed another chance when he could not connect properly from Invincibile's cross to the back post.
Killie were made to pay in the 84th minute when Aberdeen levelled through McDonald after Brown had fumbled a Mulgrew free-kick into his path only three yards from goal.
There was still time for Langfield to make a crucial save from Russell before Brown made a fine block from Maguire at the other end in a barnstorming finale.