"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 Argentine limped off to be replaced by Gabriel Jesus, the club's only other recognised central striker.
While second-placed City have next to no chance of catching leaders Liverpool, who have a 20-point lead with eight games remaining, the absence of Aguero will be a blow to Guardiola's Champions League hopes.
City lead 2-1 against Real Madrid from the away leg of their last 16 match and are hoping to reach August's 'Final Eight' of the competition in Lisbon.
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