McArthur looked to have given Palace a lifeline when he nodded home a Yannick Bolasie cross when City were leading 2-0 at the Etihad Stadium.
The goal was ruled out for offside, but replays showed the former Wigan Athletic man was clearly onside.
Yaya Toure added a third goal and struggling Palace have now won only one of their last 11 games in all competitions.
Palace boss Warnock was at a loss to explain why McArthur's effort was ruled out and pulled no punches with his verdict on the decision.
He told BBC Sport: "We worked so hard at the Etihad. Two goals down and you score a good goal like that, it knocks you. I don't know why top class officials get it wrong.
"It wasn't even close. It was a disgraceful decision.
"The linesman will be disappointed when he sees it. It's not hard to look across and see it. We might have lost 5-1 - I can't tell you that, but at 2-1 the crowd might have been nervous.
"We worked so hard all week - it's nothing to do with us that the goal was chalked off."
