The Austrian, a summer signing from Werder Bremen, had put the Potters ahead against Manchester United just before half-time, but was forced off early in the second period
The Austrian curled home an excellent free kick as Hughes' side went in at half-time 2-1 up, but, having suffered from illness prior to the game, he had to be substituted in the 49th minute.
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"They had the vast majority of the play in the second half," Hughes explained after the defeat.
"We lost the ability to take the fight to them in the second half when Marko Arnautovic went off. So that affected us. Even so I didn't think they were creating a great deal.
"He was ill unfortunately; just before the game we were aware he might not complete the game.
"At half-time we thought he might have to come off but he wanted to continue. Unfortunately he could only last 10, 15 minutes."
Arnautovic's goal was his first for Stoke in his seventh outing since moving to the Britannia Stadium.