The result has given Antonio Conte's side a 13-point lead at the top of the table, and Hughes believes that the Blues will not relinquish the title at this stage.
Hughes told BBC Sport: "We are desperately disappointed we did not get anything out of the game. The ball dropped kindly for them and they got the winner.
"It is Chelsea's title now and you could see from their celebrations we ran them close. We have given a good account against the champions-elect.
"We kept on going, kept on moving the ball but there was a suggestion for a red card for our penalty. It was a little bit feisty, we gave everything and I cannot criticise our players."
Stoke, meanwhile, remain ninth in the table.