The midfielder was struck on the side of the head by a clearance from Marcus Hall and was stretchered off with less than two minutes on the clock.
The good news from the hospital is that nothing is broken but Hughes will miss Tuesday's night's trip to Burnley and the first ever City away league game at Scunthorpe next Saturday.
Chris Coleman told the club website: "We had an initial worry when Stephen went down injured because he has obviously broken his jaw this season already.
"His mouth was cut quite badly but it doesn't look as though anything is broken. "You always fear the worst when a player goes down and doesn't move but we were quick to attend to him and it was only right that he went to hospital.
"He is suffering from a bit of concussion which will rule him out on Tuesday but we'll see how we go from there."