Potters boss Hughes was in the Chelsea team the last time Stoke beat the Blues, in a League Cup game in 1995, while their most recent league win had come back in 1975.
Andre Schurrle gave the visitors the lead after 10 minutes at the Britannia Stadium but they could not extend their advantage, with Ramires particularly culpable.
Schurrle struck again within three minutes to level things up, and it looked set to finish all square until substitute Oussama Assaidi unleashed a superb drive into the top corner in the 90th minute to earn Stoke a 3-2 win.
Hughes said: "It was a great result for us. I thought it was a fantastic game. From start to finish we put in a real performance.
"We had to recover very quickly from the disappointment of going behind in the game. I thought we showed real character and we stuck at it.
"Chelsea gave us a little bit of a runaround in the first half and we had to hang on in there, but that's what we did.
"In the second half I thought we were excellent, and the two goals we scored were absolutely outstanding.
"It was another blow having got our noses in front to concede almost immediately. That was a test of character as well but we stuck at it.
"From our point of view it's a huge result because we've set our standards and we need to maintain them."
Assaidi is on loan from Liverpool for the season, and chose some way to score his first Premier League goal.
The 25-year-old had been disappointed to be left out of the starting line-up and only replaced Jonathan Walters with six minutes to go.
Hughes said: "I did say to him, 'You need to be ready if called upon, you need to come on and make an impact' - I didn't anticipate he was going to make such an impact but I'm glad he did."