A win at the Etihad on Saturday would have seen Man City crowned Premier League champions, and Aguero had a golden chance to put Guardiola's side on the road to that result.
With City leading 1-0 just before half-time thanks to a Raheem Sterling goal, Aguero stepped up to take a penalty which Gabriel Jesus had won - but the Argentine forward made a mess of the opportunity.
City's record goalscorer embarrassingly chipped an attempted Panenka-style spot-kick straight at Edouard Mendy - and the miss proved costly as Hakim Ziyech and Marcos Alonso scored after the break to ensure Chelsea won the Champions League Final dress rehearsal.
The result should do little to prevent City actually winning the title, but they must put the champagne on ice for now - and City boss Guardiola said it was unfair to label Aguero selfish for taking the penalty the way he did.
"He is selfish because he misses, if he scores he is a genius," Guardiola told reporters. "That is the reality. Always I say to the players with penalties take one decision - Panenka, right, left, short, whatever you want - but commit. He was convinced.
"He is a sensible guy and we are not going to talk about what Sergio has done. He took the decision and that is all. The takers have to take responsibility and he did it.
"Everyone is disappointed but the first disappointment is him."
Despite no personal blame from the boss, Aguero admitted he was sorry for the miss and took ownership after the match.
He wrote on his Twitter account: "I would like to apologise to my team-mates, staff and supporters for missing the penalty. It was a bad decision and I take full responsibility."
Guardiola, however, was convinced City should have had a second penalty shortly before Alonso's winner when Sterling went down as he was challenged by Kurt Zouma.
"It is a penalty, that is all," Guardiola said. "After you have to score, of course, but what can I say? Nothing."
Despite the frustrating result it surely remains only a matter of time before City do clinch the title.
It could even be secured before their next game against Newcastle on Friday if second-placed Manchester United drop three points from their three games over the coming five days.
Guardiola said: "We are sad we lost, we wanted to close out the Premier League but we have to be focused. Football is unpredictable and we have to focus on the game at Newcastle."
Additional reporting by PA.