The Owls boss was convinced goalkeeper Chris Kirkland had been fouled by Marvin Elliott as he came off his line to intercept a cross.
Sam Baldock volleyed home the loose ball to give bottom club City a point they deserved and Jones could hardly contain his anger with referee Darren Deadman.
"It was a forearm smash by Elliott. Anywhere else on the pitch it would have been a free-kick," he said.
"We had taken everything City could throw at us and all you ask is a fair deal from the match officials.
"We have had trouble with this referee before. If he had done his job we would have been going home with three points, but I get tired of saying that sort of thing.
"We scored a great goal and Chris Kirkland has hardly had a shot to save. I feel so frustrated for my players.
"The relegation battle is going down to the wire. But we already knew that before this game."