Ryan Bennett was given a chance to shine ahead of the 27-year-old centre-back, who suffered an injury-wrecked pre-season and has struggled to find any consistency.
But Canaries boss Hughton said he needed to change things after their humiliating 7-0 hammering at Manchester City a week earlier.
"It is always a big decision to leave a player out, but I just felt after the last few games I wanted to change things and certainly Ryan has been one who has been pushing, and pushing hard," Hughton told the Eastern Daily Press.
"He played very well at Stoke, but Seb is a fine player and I think where he perhaps has found it difficult is he missed the whole of pre-season and he has found it hard to get that consistency.
"He will do, though, and he'll be pushing as hard as he can to get into the team.
"Sometimes you can just change things to improve the mentality of the team and I felt after the Manchester City game we needed to do that."