Cisse, 30, has scored five goals and been sent off twice in his seven QPR appearances since his move to Loftus Road in the January transfer window, and Hughes has been happy to deal with the dismissals if the former Liverpool striker's goals help the club survive.
"I'm delighted for Djibril," he said.
"Obviously it has been a little bit stop-start for him and invariably when he has played and been on the pitch he has made an impact in terms of scoring and been involved in key moments.
"We left it late. We played a little bit stop-start and it was difficult to replicate the momentum we've generated in recent weeks. You hope that something will happen and thankfully it did."
He said: "It was a more difficult chance than it appeared, I think the fact that Djibril just dispatched it so nonchalantly took away from how difficult the chance actually was.
"A player like Djib, that is food and drink to him and thankfully he converted it. It was great for us, we left it late and it wasn't a great game - the momentum we have been able to create in recent weeks was hard to replicate."