The Argentine, 24, was carried off on a stretcher after eight minutes following a challenge by Nathaniel Clyne.
Aguero tweeted that it had been a “tough hit” to his right knee but
said there was “no significant injury”.
He added that he would find out more about the injury on Monday and also discover how long he would be out for.
Aguero has become a key player for City, scoring the goal that gave them a 3-2 victory over QPR on the final day of last season to secure the Premier League title.
He scored a total of 23 league goals in his debut season following last summer’s £38m move from Atletico Madrid.
Aguero was replaced by Edin Dzeko on Sunday. The Bosnian scored the equaliser as City came from 2-1 down to beat Southampton 3-2 at the Etihad Stadium.
City manager Roberto Mancini said his side deserved to win the game but felt his players wasted several clear-cut opportunities to build on their lead.
“The big problem was we missed five or six chances when we were 1-0,” said the Italian. “Then it changed.”
Carlos Tevez broke the deadlock on 40 minutes before Southampton hit back after the half-time interval to take a shock lead through Rickie Lambert and Steven Davis.
Dzeko levelled on 72 minutes and Samir Nasri, who had set up Tevez for the opener, scored the winner with 10 minutes remaining.
“We deserved to win the game,” said Mancini, whose side’s next league outing is against Liverpool at Anfield next Sunday.