Willian's near post free-kick beat Lee Grant to hand the Premier League leaders the breakthrough early on, but Jonathan Walters struck level from the penalty spot shortly after Bruno Martins Indi had seen a goal ruled out.
Chelsea dominated the second-half and continually went close, Marcos Alonso's free-kick coming back off the crossbar while Grant saved from Pedro and Nemanja Matić.
Yet captain Gary Cahill - the man who conceded the penalty on Walters in the first-half - popped up with the winner three minutes from time after Erik Pieters couldn't deal with David Luiz's header and Cahill stabbed high into the top corner to seal the three points.
Our performance deserved a point, says Stoke manager
Yet Hughes felt that his Stoke side had done enough to earn a point, saying afterwards in his post-match press conference: "When you get to that stage of the game, with three minutes to go, I thought we'd done enough.
"I think Chelsea would've been more than pleased with a draw out of that game given the way it panned out so to not get anything is a little bit hard to take.
"When the goal went in, I saw the reaction of everybody connected to Chelsea, they were absolutely delighted to get maximum points. Maybe that was a little bit fortunate in my view.
"The goals themselves are disappointing, clearly the first one - Willian has got that ability to produce balls that are right on the money and he's done it. He tested Lee and unfortunately it's a gone in.
"We had a good response, clear penalty going the other way. Cahill was a bit fortunate to stay on, I think he was the last man so you could argue that it was maybe a red card.
"I thought the goal that was chalked off, there was a little push on [César] Azpilicueta from Saido [Berahino], but he would never have got anywhere near the ball that actually went on Bruno's head and he dispatched it so we were a little bit unfortunate there.
"All in all, we get to 87 minutes and we've just played Manchester City and Chelsea back-to-back and after there were a few questions were asked of us after Spurs - rightly so - I think we've answered all of those in our recent displays.
"We can take some comfort from that, although ideally we wanted to take something out of the game because I think our performance deserved that."
Hughes denies Stoke targeted famed Chelsea hothead Costa
The Welshman was asked about Stoke's battle with Diego Costa throughout the 90 minutes, with the Spaniard going head-to-head with Martins Indi throughout.
Yet Hughes rejected the idea that they attempted to wind up the striker, explaining: "People are trying to say that we targeted him and we didn't do that, absolutely not. It's more likely he targeted our players to be perfectly honest.
"We wanted a competitive game - that's what it was. I really enjoyed it, it was a really good Premier League game with no quarter given or asked.
"I played in that position for many, many years and I look at his quality as a striker and he's an outstanding striker but on occasions he's got element of his play that he doesn't need to have really.
"You can still have an edge and an element of your play where you can look after yourself but you don't have to have the rest of it, I think it takes away from his performance and his image as a player.
"It's not necessary, but maybe that's how he generates his feeling in the game where he's able to produce his best work, maybe, and he needs that element to his play but I just think it detracts from what a good player he is."
Asked whether he felt Costa went to ground too easily, Hughes added: "Yes, clearly, on numerous occasions and he stayed down when there was nothing wrong with him. We don't need that."
Bardsley dismissal was 'one of those' acknowledges Welshman
Hughes took little issue with Phil Bardsley's stoppage-time sending off, handed a second yellow for a late tackle after picking up an earlier booking for a poor challenge, but believed perhaps greater scrutiny on Anthony Taylor's decisions meant a number of Chelsea players were fortunate to escape similar treatment.
The Stoke boss said: "I've not seen it, it's only a yellow card. Maybe it is a little bit of frustration that he's taken the lad out. Second yellow card, quite possibly. It's unfortunate.
"I've just said downstairs - if you want to be a little bit pedantic about it - clearly there was a lot of emotion flying around the place when they scored the winner and a lot of their players flying into the crowd and whatever were on yellow cards, and they were a little bit fortunate in terms of not getting red cards themselves.
"Hey-ho, it's one of those. We're disappointed, we thought we deserved something from the game, and we haven't but we take credit from going up against Manchester City last time and Chelsea today and we've done okay."