Thomas drilled home a free-kick early in the second half to give the Dumfries side’s play-off hopes a boost with Palmerston assistant boss Dougie Anderson saying: “The game could have gone either way but our players showed a lot of resilience and character. We knew that in terms of the top four we needed a win and we achieved that.”
The Doonhamers pressed early and home goalkeeper Scott Gallacher did well to grab a Stephen Dobbie drive and the visitors claimed to have scored after 11 minutes but their celebrations were cut short.
Referee Stephen Finnie spotted Kyle Jacobs forcing the ball home with his arm and promptly booked the midfielder.
The Sons created danger on 18 minutes when Danny Handling curled in a shot from 20 yards that saw Jack Leighfield scramble across goal to save with Sam Wardrop denied with a follow-up effort.
Dumbarton came close again on 25 minutes when Liam Dick slotted the ball past Leighfield however Darren Brownlie popped up on the line to clear.
Despite being on top, the hosts almost gave themselves a sucker punch on 33 minutes when Mark Stewart cut out a Callum Fordyce cross with a header that only just missed his own goal.
The deadlock was broken three minutes into the second half when Thomas cracked home a low free kick from a tight angle and Queen’s almost doubled their advantage within a minute however a cute Dobbie chip hit the bar and bounced to safety.
An equaliser should have arrived on 67 minutes when Dobbie used a hand to block a Liam Burt free-kick but Nisbet sent the resultant penalty over the bar and out of the ground.
Dumbarton pushed for the equaliser they deserved but Leighfield kept them out with fine saves from Andy Dowie and Dimitris Froxylias with Finnie refusing to award a second spot-kick when Burt looked to have been fouled.
Sons boss Stephen Aitken said: “I cannot criticise the players at all for the effort they are putting in and the creativity they are showing, however if you do not score goals you do not win games.
“They put everything into the game but things are not falling for us in front of goal.”