Barton is set to face Football Association disciplinary chiefs next week after admitting a charge of violent conduct against former team-mate Ousmane Dabo, was drafted into Saturday's squad.
Keegan sent the ex-Manchester City man on for the closing minutes and within seconds made a strong challenge on Gunners winger Samir Nasri.
Keegan had words with both Nasri and also Arsenal captain William Gallas at the final whistle.
Keegan: "Joey came on, got a good tackle in on Nasri. Then the guy sliced him down. That's what happened and that's what I saw, which is what I was upset about.
"I like Nasri very much - he's a player we looked at for a possible signing but you can't do that.
"If it had been the other way round, I wonder what the reaction would be.
"I know the referee didn't see it but the linesman did and it should have been a red card.
"I will tell Arsene Wenger the same thing when I see him.
"It wasn't a reckless tackle - it was a good tackle.
"We want to see the good players play, but we want to see good tackles as well.
"Joey has done nothing wrong. I'm concerned about my team, not individual players."