The Ivorian, one of City’s best and most consistent performers this season, limped off during the first half of City's 3-2 defeat against Liverpool.
Toure was replaced by Javi Garcia on 19 minutes after appearing to tweak something following a shot and manager Pellegrini told reporters after the game that the injury could rule the Ivorian out for the rest of the campaign.
"It will be difficult for Yaya Toure to finish playing this season,” said Pellegrini.
Pellegrini insisted his team can still regain the Premier League title they lost last season despite the defeat at Liverpool.
The result left them seven points behind the Merseysiders with two games in hand, the first at home to bottom club Sunderland on Wednesday.
"We are still going to fight," the Chilean told Sky Sports.
"A lot of things will happen between now and the end of the season. If we win our two games in hand we will be a point behind Liverpool, who still have to play Chelsea. The title does not finish today."
Pellegrini, who joined City from Malaga last May, has said it would be "bad for football" if Chelsea won the title because they are too defensive but he was more complimentary about Liverpool.
"It was a very pretty match as it was two teams who like to attack," he said. "We deserved a better result. We are very unlucky.
"We played very well second half when there was only one team on the pitch and we had clear chances to win the game. They also played very well, especially the first 20 minutes.
"There was a clear penalty when Martin Skrtel had a handball but I don't think the result today was because of the referee, who had a good game."
Four of City's final six games are at home, where they have won 14 of 15 League games this season. After hosting Sunderland they entertain West Bromwich Albion, then play away games at Crystal Palace and Everton before home matches in the final week of the campaign against Aston Villa and West Ham United.
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