The City manager saw his side's five-match unbeaten run come to a grinding halt at Stamford Bridge, where the visitors struggled to trouble Jose Mourinho's title challengers.
Mohamed Salah, Frank Lampard and Willian were all on target for Chelsea, who gained a measure of revenge for Stoke's 3-2 win at the Britannia Stadium in December.
"I was disappointed with what we produced," Hughes said. "It's a wake-up call to us. For weeks and weeks we've been a lot better than that but for whatever reason we didn't have enough players playing at their maximum today.
"In the end we weren't able to ask enough questions of a good Chelsea team and they didn't have to get out of second or third gear to take the game away from us."
The hosts came into the contest following back-to-back losses against Crystal Palace and Paris Saint-Germain, but Hughes did not expect anything less than a stern test at a ground where Stoke have never tasted victory in the Premier League.
"They (Chelsea) carry a strong squad and the players who come in are high quality," he said.
"Off the bench they can bring quality players on just to take the game away from you. It was always a big ask to come here but I expect my team to do better than they did.
"We have to pick ourselves up."
‘We were in Amsterdam, so I faked a toothache to go and see Crystal Palace in the FA Cup final. I couldn’t make the replay, though – the Stones worked it out’: Rolling Stones guitarist Bill Wyman feigned injury to watch 3-3 draw with Manchester United
‘Home truths needed to be spoken at Manchester United and Ruben Amorim has been brave enough to do that – the way he’s dealt with Marcus Rashford has been correct’ Former Red Devils star praises new boss
