Jonny Howson's first-half strike proved enough for the Canaries to get a first away league win of the campaign, although Stoke were left believing they might have got something more after Jones fell under Fer's challenge in the second half.
Fer pulled at Jones' arm as he tried to get on the end of a cross, and afterwards the summer signing admitted his guilt.
"I pulled his shirt a little bit," Fer told Sky Sports.
"Just a little bit. It happened."
Regardless, Norwich were left celebrating a much-needed three points ahead of a run of fixtures that sees them face Chelsea, Arsenal and Manchester City in three of their next four games.
"We dug in well at the end and limited their chances," Howson said.
"We set the tempo with the way we started the game. That set us up. In the second half we had to dig in at times."
Howson's goal in the 34th minute capped a period of pressure for the visitors.
"We'd had a few chances before then and hit the bar," added Howson.
"That always helps when you are on top. It gives you that confidence to throw a few more people forward. We could have had more on a different day."