Motherwell booked a Premier Sports Cup semi-final spot for the second season in a row after Regan Charles-Cook's fine strike piled further pressure on Aberdeen manager Jimmy Thelin.
Charles-Cook - who signed on a free transfer in the summer - smashed a first-time effort into the far corner from the edge of the box having been teed up by Emmanuel Longelo.
Aberdeen have now failed to score in five of their six domestic matches this season as well as being bottom of the Scottish Premiership with just one point.
Motherwell played out from the back confidently as they have all season under Jens Berthel Askou and almost went in front in the first half when Tawanda Maswanhise's powerful drive came out off the post.
Thelin's side also had chances in an entertaining contest, but failed to truly test Calum Ward in the Motherwell goal.
Kevin Nisbet and Jesper Karlsson both fired wide before the break, while centre-back Mats Knoester and substitute Nicky Devlin were both denied by the crossbar.
Despite nervy moments late on, Motherwell clung on for a confidence-boosting victory after a string of league draws.