The Manchester City striker, who earlier opened the scoring against the Gunners at the Etihad Stadium, had to make way for Jesus Navas shortly after the start of the second half
The Argentina international gave his side the opening goal of the game after 15 minutes but had to be withdrawn shortly after the start of the second half.
“We think Aguero has a problem with his calf. The doctor will see tomorrow how many weeks he will be out," Manchester City manager Manuel Pellegrini said after the match.
It was the second major injury of the match as Gunners defender Laurent Koscielny was stretchered off with a "deep laceration" to his knee, suffered in an unsuccessful challenge as Alvaro Negredo netted the hosts' second.
City are now three points behind Premier League leaders Arsenal after 16 matches played.
Aguero's early strike was his 19th of the season in all competitions, with the talismanic forward averaging one goal for every start in 2013-14.
He netted six goals in five games as Manuel Pellegrini's side reached the knockout stages of the Champions League for the first time.