Kompany has sat out City's last four matches since limping out of the Champions League defeat to Juventus in the middle of September and will again be absent on Saturday when Newcastle United travel to the Etihad Stadium.
The 29-year-old was called up to the Belgium squad for matches against Andorra and Israel on Friday morning, but while Pellegrini says he cannot stop his captain from travelling, it would be impossible for him to play a part on the pitch.
"Vincent continues to recover from his calf injury and we will see the way he improves the coming weeks," he told a press conference. "Vincent cannot play for Belgium."
Asked whether he would pull his captain out of international duty, Pellegrini replied: "No, I can’t ask him not to travel, if he is called he must go, but he cannot play so I don’t think he will play.
"He is an important player. He must be with his mates. Belgium is playing important things for the next European Cup. That was not a problem for him to go to the national squad."The Chilean also revealed Yaya Toure is among five players not able to feature on Saturday, a list which also includes Gael Clichy, Fabian Delph and Samir Nasri.
Toure was withdrawn early in the second half of last weekend's heavy defeat at White Hart Lane with a hamstring injury, but started the Champions League clash with Borussia Monchengladbach on Wednesday.
The Ivorian midfielder had clearly not recovered and was substituted at half-time in Germany, where City went on to overturn a 1-0 deficit to win 2-1 and pick up their first points of this season's European campaign.
Pellegrini was pleased to see his team recover in that manner, as he says he has become tired of hearing about his side's supposed lack of spirit and desire.
"So many times I must read or hear this team has no character to play in Europe because we lost against Juventus, but we won against Bayern Munich away, we won against Roma away so I think this team has character," he continued.
"It was important to demonstrate when you don’t play very well that you have another way to win.
"It was very important because it is very difficult to qualify if you don’t have any points from the first two games. Maybe we didn’t deserve to lose here against Juventus but we did. Maybe there we won in the last minute.
"I am very happy with the character of team. It is not easy to come from 1-0 down and in the last 30 minutes to play the way we did so that demonstrates we have a strong team with strong character that plays the same way in Europe as we do here."