The former Barcelona player won a fourth-minute spot-kick with an excellent solo run into the box which drew a foul from Ashley Williams, before confidently beating Lukasz Fabianski from 12 yards.
That goal was Bojan's second of the campaign after he missed the latter half of last season with a serious ACL injury sustained in a January FA Cup victory over Rochdale.
Hughes was thrilled with the 25-year-old's showing at the Liberty Stadium and thinks he will be a big boost to Stoke's chances of a success as he continues to find his full match fitness after returning to the pitch in August.
"We are delighted with his performance," said the manager. "Obviously he made the difference and he was able to get the key moment and dispatch the penalty.
"He has probably come back quicker than we thought he would. For him to be playing regular football now so soon after the injury that he had just shows how hard and how professionally he approached a really serious injury.
"He was determined to get back as quick as soon as he could. He did everything and more in terms of his rehab. We hope and expect that he will reap the benefits of that and so will we this season.
"Last year he was having a massive effect on our performances and results. To lose him when we did was a big blow but to get him back so early is a real bonus for us."
After failing to win any of their first three league games this season, Stoke have now won three in a row to move up to 11th in the table.