McDonald headed home midway through the second half after Motherwell goalkeeper John Ruddy had looked set to defy Aberdeen's attempts to equalise Lukas Jutkiewicz's early opener.
McDonald then received a second yellow card for lifting his shirt over his head but it was the 10 men who came closest to claiming all three SPL points.
Former Motherwell boss Mark McGhee, who avoided the extreme abuse directed his way during his first match at Pittodrie against the team he left in June, would have been happier with his team's performance, although both teams contributed to an entertaining game amid a torrential downpour.
His successor Jim Gannon dropped Jim O'Brien to the bench after criticising McGhee for admitting the winger fitted his transfer target criteria.
Jamie Murphy stepped in to play just behind the front two while goalkeeper John Ruddy and full-backs Stevie Hammell and Yassin Moutaouakil returned from injury. Aberdeen were without the injured Sone Aluko but Maurice Ross returned from suspension.
Ross Forbes had the first shot on target of an open start to the game but Jamie Langfield was behind his 20-yard strike.
Ruddy rescued the hosts with a point-blank save from Lee Miller's header after a Richard Foster cross found him unmarked eight yards out. And Motherwell took the lead within 60 seconds when Lukas Jutkiewicz fired home his fifth goal of the season in the 13th minute.
There appeared to be little threat when the on-loan Everton forward collected the ball just inside the penalty box, but he shuffled past Foster and fired a low shot that beat Langfield at his near post.
Aberdeen almost conceded another soft goal three minutes later when Jerel Ifil failed to deal with a Ruddy kick-out, but Andrew Considine cleared Murphy's header off the line after the Motherwell youngster had lifted the ball over Langfield.
Motherwell continued to threaten with some brisk passing - Giles Coke curled just over from 20 yards and Forbes shot wide after inventive play from Murphy.
Mark Reynolds then shot just over from 30 yards as Well looked in control but Aberdeen twice came close in the latter stages of the half.
Ruddy stood up well to parry Michael Paton's powerful strike after Ross's cross found him unmarked at the back post, and Miller drilled just wide from 25 yards.
O'Brien replaced Forbes at half-time with Murphy moving wide in an orthodox 4-4-2 but Motherwell made a sloppy start and Ruddy again dived to parry after Ifil was allowed a free header from Charlie Mulgrew's corner.
Hateley and Ruddy combined to block after Peter Pawlett brought down another deep corner from Mulgrew as Aberdeen put Motherwell under pressure.
Sutton had two quickfire chances, but hit Langfield from 20 yards as space opened up and then took a heavy touch following slick counter-attacking from Jutkiewicz and O'Brien.
Miller headed over from eight yards after another set-piece from Mulgrew and the Dons left-back's deliveries finally paid off in the 68th minute when his deep corner found McDonald unmarked.
The midfielder headed inside the near post but his joy immediately turned to despair. Crawford Allan had booked McDonald in the 56th minute for pulling back Coke and gave him a second yellow card after he pulled his shirt partially over his head.
Reynolds shot just wide from 20 yards after a one-two with Sutton, who then volleyed over from a tight angle. And Jutkiewicz was too high with an acrobatic volley when he may have been better heading O'Brien's cross.
But Motherwell failed to build on their man advantage and the Dons twice came close to a late winner. Ruddy pushed away Paton's low angled drive and substitute Darren Mackie was inches away from sliding in Considine's ball across the face of goal.