John Hughes, the Raith Rovers manager, believes referee Barry Cook should have reduced Queens to ten men just seconds into the game.
First-half goals from John Rankin and Derek Lyle saw Queens home with Jean Yves M’voto replying after the break for Rovers.
However, Hughes was critical of Cook’s handling of the first-minute aerial challenge between Lyle and Rovers skipper Jason Thomson.
“The elbow in the first minute of the game was a straight red card,” he claimed. “I’m really disappointed in the referee and his linesman that they took no action on that.
“It doesn’t matter if it is the first minute of the game or the last minute and I’ve said that to the referee.”
Queens dominated the first half and carved out the first chance when Lyle’s header from a Jordan Marshall cross was blocked by keeper Conor Brennan.
The home side did go ahead when Raith failed to clear their lines following a cross into the box and Rankin took advantage with a drive into the bottom corner.
Andy Dowie nodded wide from Stephen Dobbie’s free-kick before the latter saw his fierce effort blocked by Brennan who recovered quickly to make sure Lyle didn’t convert the rebound.
Queens doubled their lead when Lyle tapped home from Joe Thomson’s knockdown.
There was hope for Raith on the hour mark when M’voto nodded home from an Iain Davidson cross but Queens held on.
Doonhamers boss Gary Naysmith said: “I told the players we needed to win and they delivered.”