City's influential captain is suspended for the visit of struggling Fulham in the Barclays Premier League after his sending off at Hull last Saturday.
With Matija Nastasic nursing a knee injury, that could mean the much-maligned Martin Demichelis and Joleon Lescott, who endured a torrid time at Barcelona last week, are again partnered at the back.
City's defence has been one of their weaknesses all season and they looked particularly vulnerable when Kompany endured an injury-hit first three months of the campaign.
But Pellegrini said of the Belgian: "He is the captain of the team, he is a very important player but we have had so many injuries during the whole year from different players and always we have managed to play well.
"I am sure the players who will play tomorrow instead of Vincent will play well."
Pellegrini also admits to having fitness concerns about Nastasic, who has missed the last eight games in all competitions with a knee injury and has been out much longer than initially anticipated.
The Chilean said: "He continues with some pain in his knee. He has at least a couple more weeks to recover.
"Of course we are concerned because the doctor doesn't know what happened with him. He made all the exams that he needs but we don't know what happened with him.
"We are taking other opinions. The doctor is in charge of that.
"The player feels a pain inside the knee but nobody knows what the pain is."
City have a tough week ahead, with the Fulham clash followed by the derby at champions Manchester United next Tuesday and then a trip to title rivals Arsenal.
Pellegrini's men also have games against Chelsea and Liverpool, the other two sides in the title reckoning, to come.
Yet for now his only focus is bottom side Fulham and what he believes could be a tricky contest.
He said: "I think it is just a very tough game. All the teams in the last position - not only in the relegation positions but in the last position in the table in the second round (of fixtures) - try to add points everywhere.
"A team like Fulham are used to defending and with Felix Magath - he always plays his teams with a lot of intensity - I am sure we need to work very hard during the 95 minutes if we want to win.
"That is why we start a very important week, but the most important game in this week is Fulham.
"I am talking to the players, trying to convince all of them it is always a difficult game.
"Maybe for important games, with the most important teams, the motivation is alone - you don't need to talk too much.
"But in these kind of games, it is very important to play from the beginning as a final."
City strengthened their status as favourites last week as they won at Hull while Chelsea slipped to defeat at Aston Villa.
That took them within six points of leaders Chelsea with three games in hand.
Despite that, Pellegrini is refusing to endorse any favourites' tag.
He said: "We continue in the fight for the title with all the other teams.
"We have to play the three games we have in hand and we will see how we play those games, but at the moment I think the four teams have the same options.
"You have to win the games (in hand) so the important thing is it just depends on what we do in the future."
City will again be without top scorer Sergio Aguero, whose hamstring injury will also keep him out of the Manchester derby at Old Trafford on Tuesday. The player will now target a potential return at the Emirates Stadium the following Saturday.
Asked about his condition, Pellegrini said at a press conference: "We don't know yet.
"Maybe next week he will start working with the squad but I don't think for the whole week.
"I think maybe at the end of the week he can be with the squad starting training."