Huth, an integral member of Stoke's squad, initially went under the knife after limping out of a home win against Sunderland on November 23.
The 29-year-old German had stepped up his recovery in recent weeks, playing in a behind-closed-doors friendly as he neared full fitness.
"Unfortunately Robert had an operation last night and he will now miss the remainder of the season," Hughes said on Friday.
"The knee was reacting adversely to the work we were trying to do with him, so this is something that we have had to do.
"He has been close on a number of occasions, but we weren't willing to risk him.
"In some regards it was good news because we have got to the bottom of what the problem was, and hopefully he will be fit and raring to go for the start of next season."
Hughes, meanwhile, appears to have accepted that speculation regarding the future of Asmir Begovic is inevitable given the Stoke goalkeeper's consistently impressive form.
"I'm not sure where the news originates from, but to be honest I'm not surprised because top teams are looking at Asmir," Hughes said.
"They will want to keep their fingers on the pulse and keep tabs of what Asmir is doing here. We aren't encouraging that though because he is somebody that we would obviously like to keep here.
"He has had an outstanding season once again, and we are fortunate that he is here and contracted to us. In that regard we are fortunate, but I know that he wants to test himself at the highest level possible."
