Central defender Johnson was involved in a flare-up with Hennessey during the home reversal against Bolton the previous week. He was dropped for the third time since his summer move from Birmingham for the clash at the Britannia Stadium but Connor is adamant it was for footballing reasons.
Connor said: "It wasn't about last week and what happened. It was more about the three goals that went in against Bolton. I made that decision on a football basis."
Johnson has struggled to reproduce his best form at Wolves and his appointment as skipper was not universally welcomed in some sections of the dressing room.
He was initially left out of the home game against Sunderland in December and then dropped again when Connor replaced the sacked Mick McCarthy in February.
Former skipper Karl Henry was handed the armband against the Potters after being stripped of the role by McCarthy last summer.
Connor said: "Karl has been at the club for a number of years and he's been a very good captain so I gave him the job.
"We were all of the opinion that someone who's done it before and knows how to do it should be given the chance.
"The decision was taken with proper consideration and for the best of the football club. He was pleased to be asked to do it again."