Things went from bad to worse for Stoke as defender Phil Bardsley received his second booking of the night for a lunge into Kenedy, and the hosts had to play 30 minutes with 10 men.
They, however, held on and clinched the tie when goalkeeper Jack Butland made a superb save to deny Chelsea's Eden Hazard, as they won 5-4 on penalties.
"Chelsea are a very good team and it took a huge effort from my guys to overcome them this evening," Hughes told the club's website after the game.
"You saw by the strength of the side that Jose picked tonight that we are respected by them and knew that they were in for a real challenge against us.
"We were able to stand toe-to-toe with them and eventually take the game away from them, thankfully."
"It has been a tremendous evening for everybody connected to the club," the former Manchester City manager added.
(Reporting by Shravanth Vijayakumar in Bengaluru; editing by Sudipto Ganguly)
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