During the closing stages of the game, Sol Bamba netted with an overhead kick, only for the official to blow up for a foul which had been committed on Cardiff defender Joe Bennett on the edge of the penalty area a few seconds earlier.
The decision denied the Welsh outfit a 2-1 lead with seven minutes plus added-on time remaining, and Warnock has suggested that the official's concentration levels "must have been minus".
Warnock is quoted by Wales Online as saying: "He's had a bad day at the office hasn't he. I like Keith, I think he's a good ref, but tonight his concentration levels must have been minus.
"Not just the goal he's disallowed, which I can accept if he blows straight away when [Bennett] goes down, but he looks where the ball's gone, carries on, looks and looks as Bamba is kicking it he blows. It's just, he'll be distraught, but that's no good to us.
"He'll get another game next week. You work hard all week and then two decisions. Because it's an obvious penalty when he moves his arm towards the ball. Two decisions in a matter of seconds."
The Bluebirds boss added: "I think he'll say he was disappointed he's made a mistake. He didn't see Sol in the box. He didn't see he was going to shoot. It's quite understandable, he's only 6ft 6ins. It's easy to understand why he can't see him."
The result in East London leaves Cardiff in fourth place in the Championship standings.