The Yorkshire club had taken the lead through Luciano Becchio, but The Blues scored all five goals in the second half to propel themselves into a semifinal tie against Swansea.
Juan Mata equalized for the Londoners just two minutes into the second period, and Warnock believes that was a turning point in the game.
"To concede as early as that in the second half against world-class players you're going to be in trouble," Warnock told Sky Sports after the game. "It was such a relief for them to get back into the game. Then they took over and were too good for us."
The former QPR and Crystal Palace manager went on to admit that goalkeeper Jamie Ashdown was to blame for Mata’s goal as it slipped through his hands and into the net.
"When you're a goalie you make a mistake and it counts," he added. "When you're anywhere else on the pitch you get away with it.
"I don't think the scoreline reflects the game but I've got no complaints. I thought it was a great cup tie for an hour."