The Ivory Coast midfielder arrived back in Manchester on Thursday after facing DR Congo on international duty in midweek.
Over 4,500 people have died as a result of the viral disease - believed to have originated in West African nation Guinea - but Pellegrini is confident that Toure's return poses no threat.
"No, really we are not concerned about it," he told reporters. "Yaya is not concerned either. I suppose he is sure about that problem - I don't think he will have any problems.
"I don't know if he was screened, but for the moment he's okay."
The 2015 Africa Nations Cup is said to be in doubt after host country Morocco reportedly sought to postpone the January competition amid fears of the disease.