The Argentine has had a setback after returning from a knee injury against Olympiacos last week and missed Saturday’s 5-0 drubbing of Burnley.
However, manager Pep Guardiola allayed fears that Aguero could be set for another spell on the sidelines.
“I am not concerned,” he told reporters on Monday.
“He didn't train. He has some disturbance in his knee, nothing serious, but he didn’t train.”
£40million summer signing Nathan Ake has recovered from a thigh injury and will make the trip to Portugal, but is only among the substitutes.
Guardiola confirmed that he was considering rotating his side against Porto, with Group C leaders City boasting a 100% record in this season’s Champions League and having already guaranteed progression through to the last 16 as a result of Phil Foden’s goal in Greece.
However, he dismissed suggestions that he would take the opportunity to hand opportunities to some of the club’s academy players as City try to make sure of top spot in the group and - in theory - an easier task in the first knockout phase.
FC Porto: Marchesin, Manafa, Mbemba, Sarr, Diogo Leite, Sanusi, Corona, Uribe, Sergio Oliveira, Otavio, Marega
Subs: Diaz, Taremi, Nakajima, Claudio Ramos, Baro, Joao Mario, Felipe Anderson, Martinez, Evanilson, Nanu, Vieira, Costa
Man City: Ederson, Joao Cancelo, Dias, Garcia, Zinchenko, Rodri, Fernandinho, Bernardo Silva, Sterling, Foden, Torres
Subs: Walker, Stones, Ake, Gundogan, Gabriel Jesus, Steffen, Laporte, De Bruyne, Mendy, Mahrez, Carson, Doyle