The Championship team prevailed thanks to goals either side of half-time from Andy Gogia and Stuart Dallas.
However, Hughes was still pleased with the run-out as he was able to feature fit-again duo Bojan and Ryan Shawcross in his side as well as new signing Glen Johnson.
Hughes told his club’s official website: “Mentally it was a big step for them, especially for Bojan, who hasn’t featured for us since January, so he will take a lot of positives from this.
“He isn’t quite up to match speed yet, but it was a good run out for him and we are delighted that he has managed to overcome this first hurdle.
“Ryan was fine – he was maybe a little bit stiff, but saying that I think we are all a little bit stiff given the fact that we had a five-hour journey down here yesterday.
“That didn’t help us, but he came through the game ok, and got a good hour or so under his belt which will help him.
“It wasn’t quite what we were looking for in terms of the result but the test itself was good for us.
“Brentford are a good side and they had a really good season last time round, and to be fair to them they look to be in decent nick at the moment too.”