Huth has not played for the first team since injuring his knee in November, which he had surgery on soon after.
Earlier this week, Potters chairman Peter Coates said it was his understanding that it was "very unlikely" the German would feature again this term.
And speaking on Friday, Stoke boss Hughes said: "Robert had an operation last night and unfortunately he is going to miss the end of the season."
Huth has missed 20 matches in all competitions since limping off in Stoke's 2-0 home Barclays Premier League win over Sunderland on November 23.
When suggesting around the time that surgery appeared likely, Hughes said the 29-year-old centre-back would be out for "a number of weeks".
Huth then made a comeback on February 25 by playing 45 minutes of a behind-closed-doors friendly.
But he has not returned to the Potters' matchday squad since then, and will now work towards trying to be fit for the start of 2014/15.
"It has been difficult for us," Hughes said.
"We tried to get him back and he has been very close on a number of occasions, but unfortunately the knee was reacting adversely to any opportunity we had to really push him on.
"Every time we tried to just push him to the next level, that is when the reaction in the knee would force us to take a step back.
"So we took him to the surgeon and he had another look at it and recommended that Robert had another operation, just to get a real understanding of what is going on in the knee.
"By all accounts it was good news in terms of what he found - there is no real structural element to it, it is just that there is an issue in the knee that is causing it to flare up and we now have a better understanding of what is going on.
"So hopefully he will be fit and well to go for the beginning of next season."