Victor Moses converted a 93rd-minute penalty at Villa Park to secure all three points for the visitors, after Mame Biram Diouf had cancelled out Scott Sinclair's opener.
Villa were punished in the closing seconds when Ron Vlaar hauled down Moses in the area, the defender seeing red before the forward completed Stoke's comeback to ruin Tim Sherwood's first game in the home dugout.
Hughes – who had seen his side lose their last two games in all competitions 4-1 – felt his side deserved take maximum points for a second successive season at Villa Park.
"We're delighted with that [result]," he said. "The key for us today was that we got the right reaction, obviously last week we disappointed ourselves and a lot of people, we needed to bounce back.
"I think we did that today. We were very positive in everything we did, I thought we were on the front foot from first minute to last.
"Obviously had to deal with a lot of positivity around the place [Villa Park], we had to take the sting out of that positivity.
"I felt we were a little bit hard done by [in conceding the opening goal], but we didn't allow it to distract us, we scored really good equaliser and in the second half thought we were the better team.
"We dealt with their threat, I thought our back four were excellent today and got their rewards.
"Victor has ability to take people on, a powerful driving run that's committed the foul, thankfully Victor picked himself up and dispatched the penalty."
