The striker was unable to train for two days this week, but did return on Friday ahead of Saturday’s game
Aguero, who has endured fitness setbacks in the wake of knee surgery, made his first league appearance since October in Tuesday’s 1-1 draw with West Brom.
He played only 14 minutes and Guardiola revealed the Argentina striker did not return to training until Friday after suffering a problem unrelated to his knee.
Asked how much Aguero could be involved on Saturday, Guardiola replied: “I don’t know. After the game he could not train, yesterday no training, today he trained.
“He trained really well but I don’t know how many minutes [he will play against Southampton].
“It’s important he can make training sessions. Unfortunately after the game he could not, nothing about the knee. Unfortunately a different position. Today he trained.”
The draw with West Brom followed a goalless stalemate in the derby with Manchester United and led to more questions about a lack of goals in Guardiola’s team.
But Guardiola does not see their issues in front of goal getting to the point where he will consider bringing in a new forward.
The former Barcelona boss pointed to the long-term performance of Gabriel Jesus and the absence of Aguero as reasons not to rush into the transfer market in January.
Jesus averages a goal every 140 minutes, putting him eighth all-time among players to have scored at least 10 Premier League goals. Aguero leads the way with a goal every 108 minutes in his career in the division.
“Absolutely not,” Guardiola replied when asked if the goalscoring woes could leave him feeling the need to add to his options up front.
“Sergio could not play much and Gabriel has incredible numbers of minutes and goals since he came here, he is one of the best in history.
“We took 13 corners last game so everyone can score goals. The way we defend depends on the strikers and the same happens up front. The strikers have more responsibility but everyone is involved to try to win games.”
Guardiola was also asked if Kevin De Bruyne could receive a rest over a busy period of fixtures.
De Bruyne has played in all but one of City’s Premier League games this season, and Guardiola made it clear he will continue to rely on the Belgium star.
“He is so important for us that he won’t rest,” said Guardiola. “He rested in the Champions League previously and right now we need him.”