“It doesn’t look good. We are going to see tomorrow. He was struggling in the last month with a problem in the knee.
“We will see what he has done but it doesn’t look good for the season,” said Guardiola.
Aguero went down under a challenge from defender Ben Mee on the stroke of halftime with the Burnley captain ruled by VAR to have made contact with his foot.
The absence of Aguero will be a blow to Guardiola’s Champions League hopes.
City leads 2-1 against Real Madrid from the away leg of their last 16 matches and are hoping to reach August’s ‘Final Eight’ of the competition in Lisbon.