The Dons hit the lead in just the third minute at Pittodrie Stadium through English-born Nigerian forward Sone Aluko who grabbed his first goal of the season with a lovely flick over 'Well defender Stephen Craigan and finish past keeper Darren Randolph.
But the visitors responded within 11 minutes when new signing Francis Jeffers leveled with a glancing header from a Craigan cross for his first SPL goal, following his stint with Rangers back in the 2005/06 season.
Motherwell looked in control of proceedings after the equaliser and managed to take the lead with just under 20 minutes remaining when Jamie Murphy made the most of an Aberdeen defensive error and slotted into the far corner.
'Well boss Stuart McCall was delighted with his side's strength of character to fight back after conceding such an early goal.
''It was all about character. We had a good word in the dressing room about not coming for a point and having a go. We knew if we won tonight we could go fifth, albeit having played a couple of games more," he said.
''When you go a goal behind so early it's easy to cave in, obviously after what happened on Saturday, but I thought in the first half we bounced back superbly.
''There were a lot of big, big performances from a lot of players, even more so when we went a goal behind against a resurgent Aberdeen side, so character was the key.''