The Bluebirds led thanks to Victor Camarasa's strike early in the second half on Sunday but Cesar Azpilicueta levelled for Chelsea with six minutes left, although replays showed the Blues captain was offside.
Ruben Loftus-Cheek stole in at the back post to head home Willian's centre in the first minute of added time to complete the turnaround and leave Cardiff empty-handed.
Warnock was involved in a touchline row with Chelsea head coach Maurizio Sarri at 1-1 and then confronted the officials on the pitch after the full-time whistle.
The defeat leaves Cardiff five points away from safety and Warnock believes he is being punished by officials for his previous criticism of them.
Speaking to talkSPORT, Warnock said: "When I came in yesterday, she [his wife] said: 'If you had wanted to thump the referee and linesman I wouldn't have stopped you'. It was so unjust.
"You could imagine what the dressing room was like. We played so well and I'm really proud of them, but once again we've been kicked in the teeth.
"We've worked our socks off for three weeks to get where we were because we thought we could beat Chelsea and we did everything right, but then a human error like this?
"The linesman yesterday said sorry to me after the game, but it's too late, what good is an apology? We're having too many honest mistakes and it's always the top teams who get the decisions.
"You just feel it's such an injustice, and I've felt like that ever since Christmas. You almost begin to think: 'is it me? Is it payback time for all the years I've shouted at referees? Have they all got together now and said, 'let's get him out of this place?'"
Warnock then directed his ire towards Professional Game Match Officials Limited (PGMOL) chief, Mike Riley, who he believes is training officials to be "robots".
"I just don't think they're educated enough at the top level," he added. "I don't think things will change now until Mike Riley goes, which is very unlikely because he's got himself rooted so far in.
"They should have better coaching. Mike Riley is in charge of referees but as a referee, he was like a robot, he had no feelings and he didn't know anything about the game.
"Like Bill Shankly used to say: 'You know the law, but you don't know the game'. That’s how Mike Riley was, and he's training all his referees now. They're all the same, they're trying to be robots."
Warnock takes his side to title contenders Manchester City on Wednesday.