Aguero’s last act of the game was to win a penalty, but as a result of Ben Mee’s challenge, he couldn’t continue any further.
“It doesn’t look good,” said Pep. “It is something in the knee. We will see tomorrow and will see what he has.
“He felt something in his knee and he will struggle in the last month, but we will see.
“The doctor said tomorrow we will know more, but it doesn’t look good at this moment.”
On a brighter note, the City boss was pleased with the way his side went about recording a second straight win since the restart.
And he was happy with the performance of Phil Foden, who scored twice and had a hand in two more during the 5-0 win over Burnley.
“We played really well and it was a good, solid performance, especially at the beginning," said Pep.
"We gave a good advantage over fifth for qualification for Champions League for next season.
“We are so close to qualification.”
Asked whether he thought this was Foden’s best display yet, Pep added: “I'm happy with him and if he feels it’s his best performance - perfect.
“I said many times, he’s never played bad. Especially for his behaviour and attitude,
“On the pitch, training, he loves to play football.
“He plays every time with us since he was promoted to be the senior squad and has played a high level
“We cannot forget he is just 20 years old. He will be decisive player for this club. “
David Silva was again at the heart of everything in City’s win, scoring his 75th goal for the Club and playing a huge part in Foden’s second goal.
Pep promised that he will be given a legend’s farewell when the fans are allowed back to the stadium
“We are going - when its possible for people to come back to Etihad Stadium - to try and have not one empty seat for this incredible legend," said the Catalan.
“For him, Joe Hart Vincent Kompany, Yaya Toure, Pablo Zabaleta… these players brought the club to another level. They deserve it.
“The situation is what is it is, but David is unique.”