Ryan Stevenson’s strike and a Garry Fleming penalty clinched victory for Sons, with Derek Lyle grabbing a consolation for the Doonhamers.
Dumbarton are up to eighth in the table and Aitken said: “I’m exceptionally proud of the players and the performance as it was always going to be difficult coming here.
“We’ve lost just one of our last six games which is good going in any division, but it seems to be covered up and that we’re not doing well.”
Queens made a good start as they aimed to bounce back from their Scottish Cup defeat at Albion Rovers – a result which cost them the chance to face Celtic.
Stephen Dobbie was off target with two free-kicks either side of unleashing a shot which was saved by Dumbarton keeper Alan Martin.
The Doonhamers were denied again when Grant Anderson’s effort was blocked by Martin before Sons struck twice ahead of the interval.
First Stevenson, pictured, found the top corner of the net after taking aim from 30 yards before Fleming doubled the lead with a thumping finish from the spot after referee Gavin Duncan awarded Dumbarton a penalty for Jamie Hamill’s challenge on Robert Thomson.
Queens pulled a goal back late-on when Lyle turned home Dobbie’s cross as new manager Gary Naysmith watched from the stands.