The Dons, who twice hit the woodwork in a vain search for a late equaliser, now trail Dundee United, who won at Partick Thistle, by four points at the bottom with three games left.
Aberdeen fell behind to Shaun McSkimming's first goal for Motherwell, after a well-worked move beginning with a run by Jamie Dolan and flicks by Dougie Arnott and Tommy Coyne. Billy Dodds hauled the Dons level four minutes later from a Duncan Shearer flick from Joe Miller's cross.
Shearer had two further efforts to put Aberdeen in front before Dougie Arnott grabbed the 58th minute winner when Brian Irvine sliced his attempted clearance of Eddie May's cross straight to the Motherwell striker.
The stand-in striker, Brian Welsh, scored twice at Firhill to ease Dundee United's relegation worries. The defender has been converted into a forward by Billy Kirkwood, and he rewarded United's new manager with his first win in his fourth match in charge, which lifted his side to within a point of Partick and Hearts.
South of the border, Bournemouth increased their chances of avoiding relegation from the Second Division by beating play-off contenders Bristol Rovers 2-0, with a goal in each half from Mark Morris and Steve Jones. In the Third, fourth-placed Bury kept up their challenge with a 3-0 win at Wigan, whose manager, Graham Barrow, was dismissed from the dug-out for dissent. Phil Stant scored twice for the Shakers.
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