In an uneventful game that seemed to be petering out into a scoreless draw, Cisse came off the bench to bury an 89th-minute winner.
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."
Hughes admitted the two red cards Cisse had been issued - against Wolves and Sunderland - have not helped but his goalscoring capabilities have made up for that.
"The reverse of that is that we have lost him for a number of games through suspension and we have to acknowledge that has hurt us this year," he said.
"To be fair the one guy you would want to be on the situation we found ourselves in, with a guy in the box waiting to get on to the end of a chance, is Djibril because he is an outstanding finisher and has been involved in key moments like this throughout his career."
Cisse coolly slotted home after Anton Ferdinand flicked Adel Taarabt's corner into his path and ex-frontman Hughes praised the finish.
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."
The narrow victory, coupled with West Brom's draw with Bolton, means QPR are now two points clear of the relegation zone with a trip to title-chasing Manchester City on the final day of the season - something former City boss Hughes has had his eye on for a while.
He said: "That (the Bolton scoreline) filtered through from the crowd, they were magnificent again.
"I have been to many grounds all over the world and the atmosphere they generate here just by virtue of the intensity and the emotion that seems to be expended here is outstanding.
"It would be a fantastic story if we were able to go there and get something, they are going for titles and we are trying to stay in this league.
"I think to be honest I probably looked at the fixtures we had when I first got the job and that one loomed quite ominously in the distant future, but it is upon us now and we have still got an opportunity to stay in the league by our own effort."
QPR captain Joey Barton will also face his former club next weekend and like Hughes he praised the home fans.
"The atmosphere was electric, it gives us such momentum. A lot of people wrote us off because our run- in was difficult," he said.
"We stayed compact as a unit. We are still masters of our own destiny. We are looking forward to a massive game."
Stoke boss Tony Pulis praised his players' approach but was disappointed with the lack of finishing.
"I was disappointed today [Sunday], I don't think it was a game we deserved to lose," he said.
"I don't think anyone could question the players' attitude and application.
"When we've got in there we've not hit the target, I don't think we made the keeper make the save, though we created some great opportunities. There's about four or five chances where you'd expect us to score."