Henry was the subject of sarcastic cheering when he was taken off by Wolves boss Mick McCarthy after 58 minutes and replaced by Adlene Guedioura.
Johnson has waited until now to voice his disapproval and believes Henry does not deserve such treatment after his lengthy service with the club.
He told the Wolverhampton Express and Star: "I thought it was a disgrace, disgusting. It stinks.
"If the fans want to have a bitch at me about it then fine, but I thought they were bang out of order.
"There are no reasons for that and it should never happen - and, for someone who's served this club so well for so long and been captain, it was undeserved.
"It's not going to help anyone."