The pair were involved in a hearted first-half exchange before the Black Country outfit collapsed to a defeat which sees them six points short of Premier League safety.
Johnson had landed himself in trouble in March when he turned up for training while under the influence of alcohol, but Connor, in charge at Molineux until the end of the season, has no intention of discarding his skipper.
"Roger's very much part of what we're doing," he told The Express and Star.
|WOLVES TO HOWL ANOTHER DAY?
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The 49-year-old also denied that the disagreement had had an effect on Johnson as he conceded a second-half penalty and failed to mark Kevin Davies as the Bolton striker netted what proved to be the winner.
"It was dealt with at half-time," Connor continued.
"Those mistakes - if they are mistakes - are in isolation and nothing to do with what happened with Wayne at all.
"He's listened to what's been said and has worked along with his team-mates."