Assaidi's superb long-range effort sealed the points for Stoke in the 90th minute after Andre Schurrle's second for Chelsea had cancelled out goals from Peter Crouch and Stephen Ireland.
The Liverpool loanee had been left on the bench for the visit of Jose Mourinho's men, but Hughes was delighted with the influence the Morocco international was able to have as a substitute.
"I disappointed him (Assaidi) today because I took him out of the team," Hughes said.
"I did say at the time 'you need to be ready, 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."
Hughes' men moved up to 12th in the Premier League with the win, and the Welshman is hopeful Stoke can maintain the level of performance they produced against Chelsea regularly.
"I just thought from start to finish we put in a real performance," Hughes added.
"We had to recover very quickly from the disappointment of going behind early in the game, I thought we showed real character and we stuck at it.
"Chelsea gave us a bit of a run around in the first half, second half I thought we were excellent, and the two goals we scored in the second half were outstanding.
"We needed to hang on in, but the longer the game went on, the more I felt we could take something out of the game.
"From our point of view it's a huge result, because we've set our own standards today and we needed to maintain them.
"If we can do that then we will be very, very difficult to overcome."
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