The Hammers looked on course for a priceless victory at Stamford Bridge when Michail Antonio gave them a 62nd minute lead but Chelsea substitute Ben Chilwell first found an equaliser before laying on an assist for fellow substitute Kai Havertz to score the winner.
West Ham thought they had found an equaliser themselves in the 90th minute when Maxwel Cornet pounced on a loose ball and fired in but VAR intervened to rule out the goal, adjudging that Jarrod Bowen had fouled Chelsea goalkeeper Edouard Mendy in the build up.
"You have seen it, it is a scandalous decision," Moyes said about referee Andy Madley after the game.
"It's absolutely rotten from one of the supposedly elite referees - it doesn't say much about whoever sent him over from VAR as well - it is an unbelievable decision against us.
"We feel we got back to 2-2 and it [the loss] was not down to anything we have done. I support a lot of the VAR stuff.
"I actually think the goalkeeper dives, he is faking an injury because he cannot get to the next one, he did the same on the first goal as well. The referee somehow gets that so wrong it is incredible."
West Ham midfielder Declan Rice also made his displeasure clear on social media after the match, tweeting: "That's up there with one of the worst VAR decisions made since it's come into the game. Shambles."
Moyes has now failed to win in 18 Premier League trips to Chelsea – the joint-longest winless streak managed by any coach at a single team in the competition (also Moyes at Arsenal).
