Aguero, 32, has only played four times since injuring his knee in June. The Argentine has featured for 12 minutes since being replaced at half-time against West Ham on 24 October.
“We will decide tomorrow. Sergio may be on the bench,” said Blues boss Pep Guardiola, whose side have already guaranteed top spot in Group C and a place in the last 16.
“He will train today and we will see the reaction tomorrow. The good thing is he has been part of the group for the last three or four days. The niggles he has had in the in past are not there.”
Champions League: Who needs what to reach last 16?
City have the Manchester derby against rivals United in the Premier League on Saturday (17:30 GMT) but Guardiola says he will not rest players against French side Marseille on Wednesday.
“We’ll play the game to win, I don’t rotate the team,” said Guardiola.
“I try to put the players in the best condition, decide the best for the specific team. There’s not one team for one competition and one for another
“The team that plays tomorrow, they can play United – or maybe not. I want to win this game, it’s not because of one more day or less.”
Reserve goalkeeper Zack Steffen could make his Champions League debut and the American said it would be a dream come true.
“Walking out and hearing the song is going to be really special for me and my family,” said the 25-year-old, who has made two City appearances, both in the Carabao Cup.
“I am excited to get out there and play another game.
“I have learned a lot so far. I feel I have got better and it has been an awesome time.”
‘Their B team could win the competition’
Ligue 1 side Marseille are bottom of the group, but could qualify for the Europa League, depending on their result and how third-placed Olympiakos fare against Porto.
Andre Villas-Boas’ men need to better the Greek team’s result but the former Spurs and Chelsea manager is not expecting any Manchester City rotation to work in their favour.
“Qualifying is not in our hands,” said Villas-Boas.
“Hopefully Porto will do us a favour but we know it is going to be hard against Manchester City. They have so many options, and so many top-level options as well.
“We cannot rely on Porto but we must be at our best to get a positive result because City’s B team are strong enough to win the Champions League.”