Lyndon Dykes’ opportunist second-half strike all but ended any hopes Morton had of finishing in the top four of the Championship and a place in the end of season play-offs.
Both sides took a while to settle before chances came in quick succession at either end. In 13 minutes Queens carved an opening when Stephen Dobbie slipped the ball to Joe Thomson but his low drive went just wide.
Bob McHugh had an even better chance for Morton in 23 minutes when a Scott Tiffoney corner fell for the striker but from six yards out he somehow scooped the ball over the bar.
Queens looked the most composed outfit and in 27 minutes Dobbie took a brilliant return pass from Dom Thomas to run in from the right, but his low 15-yard drive was superbly turned round by keeper Conor Brennan. Two minutes later Brennan was in action again to save from a Dykes header.
The Dumfries side almost made the breakthrough in 51 minutes when Thomson put Dobbie clear but his clip over Brennan hit the post.
Queens got the winner in 69 minutes when Thomas drilled the ball across goal for Dykes to stretch out a leg and crack the ball off the post, but he reacted quickly to knock home the rebound.