Terry Butcher's Well side made almost certain their own top-six finish before the league split, with goals from Kevin McBride, Jim Hamilton and Scott McDonald.
The Dons' lone strike came from Markus Heikkinen, who slotted home the rebound from Darren Mackie's saved penalty, but the visitors ran out comfortable winners.
McBride broke the deadlock from the spot after 22 minutes, beating Ryan Esson after McDonald had been upended by Phil McGuire.
Ten minutes later it was 2-0 as Hamilton lobbed in a superb second from just outside the area, with Esson unable to keep the effort out despite getting a hand to it.
The Dons soon had a spot-kick of their own after Mackie was brought down by Stephen Craigan. His 12-yard effort was saved by Gordon Marshall, but Heikkinen reacted first to net from the rebound.
However, Well wrapped up the win 18 minutes from time as McDonald beat Kevin McNaughton to the ball and curled an excellent shot beyond the reach of Esson.