Oussama Assaidi's late strike gave Hughes's side the points, and the Welshman praised his players' efforts after the game.
"Chelsea will always ask questions of you because they're an outstanding side, but I thought it was heroic at times," Hughes told Sky Sports News.
"The result has to be up there [as one of the best for me] doesn't it. There was the disappointment of going behind, but what a response it was.
"Chelsea made it difficult at times, they were excellent, but we stuck at it and we held our nerve in the second half with our anticipation and out attitude."
The result leaves the Potters in 12th in the Premier League.