Victory over the side they will face in the Champions League final in three weeks’ time would have seen Man City confirmed as Premier League champions for the third time in four years on Saturday.
But despite taking a first-half lead through Raheem Sterling, record goalscorer Aguero then embarrassingly fluffed his lines from the spot and Hakim Ziyech levelled for the Londoners after the break.
With the scores level, Sterling went down in the Chelsea penalty area under contact from Kurt Zouma - but both referee Anthony Taylor and the VAR decided that the collision did not warrant a spot-kick.
Guardiola was furious with the decision, and then had to watch on as Marcos Alonso then grabbed the winner deep into injury time from a Timo Werner cross.
Following the game, Sterling told Sky Sports: “I could not get a shot off, he put a knee into the back of my hamstring.
“I don’t know how it is not a penalty and has not been reviewed properly.
“I thought VAR was here to help, but it was not meant to be.
“The referee said it had been checked, cleared and was not a penalty, but for me it was.”
Guardiola felt the same, telling Sky Sports: “It’s (a) penalty. It has happened, football has happened, we will try the next time to score our penalty and that is all.
“The opinion for the officials and for (referee) Anthony (Taylor), they know it, that is all I can say.
“Sometimes we make mistakes, maybe they believe they did not make a mistake, and that is OK.
“I saw in the TV, it is a penalty, that is all. (In the) 88th minute, after you have to score of course, but what can I say? Nothing.
“In 21 days we are going to face them again in the final of the Champions League, we are going to learn from that.
“Now we are going to try to win the three points you need to be champions.”