Motherwell boss Terry Butcher chose to include wantaway Stephen Pearson in his starting line-up while Aberdeen boss Steve Paterson decided to make two changes to the side that beat Brechin 5-0 in midweek.
It was Aberdeen who had the better of the opening period of the match with Scott Booth and Markus Heikkinen both going close in the opening minutes.
They were made to pay for not making the most of those chances when Motherwell opened the scoring on ten minutes.
Steven Hammell's cross was latched onto by Steven Craig whose delicate lob went over the head of David Preece and into the corner of the net.
The Dons went close to equalising ten minutes later when Booth found space on the edge of the area before firing his right-foot shot just the wrong side of the upright.
Booth again went close to putting his side back on level terms with a flashing header at the near post that flew only inches over the bar.
At the start of the second half both teams were forced into changes with Chris Clark coming on for Paul Sheerin for the Dons and Motherwell bringing on Jason Dair for David Clarkson.
Aberdeen created three chances out of nothing in the space of three minutes, the first coming when Booth set up Phil McGuire on the edge of the area and his shot was turned over the bar by Gordon Marshall.
From the resulting corner the ball ended at the feet of Kevin McNaughton and his thunderous 30-yard drive produced another fine stop from the visiting keeper.
It was Marshall again who came to Motherwell's rescue when Steven Tosh was sent through on goal but the big keeper was again up to the task pushing the ball away to safety.
Motherwell secured all three points 13 minutes from time when Pearson collected the ball 30 yards from goal and drove through the heart of the Dons defence before slamming the ball low into the corner of the net.
Motherwell's day was complete in the 90th minute when another driving run by Pearson had the Dons defence chasing shadows, and when his pass found the right foot of Keith Lasley, there was only going to be one outcome as he powered the ball into the back of the net to give Motherwell a well-deserved win.