In a strangely subdued opening to the match, Aberdeen came closest to opening the scoring after four minutes when a snap shot from Stevie Crawford was narrowly off target.
Motherwell gradually got to grips with the game and should have gone ahead after 12 minutes. David Clarkson held the ball up long enough for Phil O'Donnell to burst into the Dons box. However, from the angle his fierce drive sailed over the bar.
Darren Smith had to look lively in the visitors' goal to thwart Steve Lovell after 26 minutes. The big striker, having giving his marker the slip inside the box, saw his effort charged down by the Well keeper.
After a good passage of play through Aberdeen's midfield, a shot from Scott Severin after 38 minutes fizzed just over the bar. The same player was unlucky within 60 seconds, climbing above Stephen Craigan to reach a Smith cross, only to see Smith pull off a great stop.
At the other end an in-swinging corner from Steven Hammell caused panic in the Dons rearguard before Richie Byrne hooked the ball away from danger.
The visitors took the lead after 63 minutes. A long ball from defence caught the Dons rearguard napping. David Clarkson seized on the chance to turn Russell Anderson before trundling the ball beyond Ryan Esson and into an unguarded net.
Worse was to follow after 68 minutes when Clarkson again evaded the Dons defence before neatly cutting the ball beyond Esson to make it 2-0 to The Well.
Aberdeen's day only got worse after 78 minutes when Clarkson and Byrne tussled for a loose ball, the Well man going down clutching his face. To the surprise of everyone, referee Thompson flashed a straight red card to send the Dons defender packing.
Within a minute Aberdeen were handed a lifeline. Kevin McNaughton drove at Hammell inside the area, where the defender needlessly conceded a penalty. Second half substitute Darren Mackie calmly slotted the penalty home.
Mackie again proved how much his side had missed him this season when he popped up to head home what had seemed an unlikely leveller after 85 minutes. Jamie Smith picked out Crawford on the right of the box, and his clipped ball to the far post found Mackie, who was on hand to nod home.
Clarkson should have penalised the home defence in the last minute, when he rounded Esson, but from an acute angle his shot drifted beyond the far post.