The Midlands club have had to sell a number of key players this summer, while centre back Scott Dann was left on the bench with a move to either Arsenal or Liverpool expected soon.
"Over the 90 minutes I thought we deserved the win and sending on Adam Rooney was a game-changing move," said Hughton.
"I thought he came on and displayed a lot of energy and certainly changed the game for us.
"Rooney is a lad who scored a lot of goals in Scotland but with our three strikers out of action he has had a lot of responsibility from day one in pre-season."
Birmingham next face Portuguese outfit Nacional in a Europa League qualifying match on Thursday.