The Blues thought they had overturned a 2-0 half-time deficit at Villa Park when Axel Disasi crashed home a header only for it to be ruled out for a foul on Diego Carlos in the build-up.
Referee Craig Pawson did not award the foul in real time but did so after being advised to check the pitchside monitor by VAR Christopher Kavanagh.
It puts the decision-review system further in the spotlight after Nottingham Forest accused VAR Stuart Attwell of being biased after he failed to intervene on three penalty decisions.
“Everyone that was watching the game will feel disappointed,” Pochettino said on TNT Sports.
“Two different things the referee said it was a foul and disallowed the goal and then going to the VAR to confirm.
“The referee is unbelievable and it’s ridiculous. It is difficult to accept, these type of things in the semi-final [FA Cup against Man City] two weeks ago it was handball and it was no penalty, the referee he didn’t check it.
“It is painful as it has damaged English football and I think Villa players and their fans didn’t understand why the goal was disallowed.
“They said it was foul and if you see the challenge what happened if we go into every single challenge like this it is going to be a foul and we wouldn’t finish the game with 11 [players].
“We can talk about the performance or the decision – it is damaging the game.
“I am calm and it is only to help. Now, we have to move on and it will be in the headlines with the disallowed goal.”
Four days on from their horror night at Arsenal on Tuesday, where they lost 5-0, it looked like being another difficult evening for Chelsea when they fell 2-0 down at half-time to Marc Cucurella’s own goal and a Morgan Rogers strike.
But they rallied in the second half and levelled through Noni Madueke and Conor Gallagher goals before the stoppage-time drama.
Despite blowing a 2-0 lead, Villa will see this as a point gained after looking leggy and below their best.
They moved seven points ahead of fifth-placed Tottenham in the race for Champions League qualification, but Spurs have three games in hand.
Unai Emery’s men, who have a growing injury list and a Europa Conference League semi-final to contend with, will still be favourites for the top four as the London club have Arsenal, Chelsea, Liverpool and Manchester City still to play.
They suffered more injury woe as influential goalkeeper Emiliano Martinez went off at half-time with a hamstring issue, while Youri Tielemans limped off with a groin problem.
Emery said: “Tomorrow we will test him (Martinez). And with the injury with Tielemans, we will wait for tomorrow. Hopefully not a lot.
“Martinez is very important – that’s clear. He saves us a lot. But Robin (Olsen) saved us in minute 90 in a man-on-man against (Cole) Palmer.
“We are very happy, even with the point we achieved today. Our way is to be consistent. And 35 matches with 67 points. Analysing the match, of course, for Chelsea were contenders to be in the top four, to have the difference we have in the table is good.”
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