The Belgium international had landed awkwardly in a training-ground collision with Micah Richards prior to the trip to Anfield, putting his participation in doubt.
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Pellegrini, though, is in no doubt that he made the right decision by selecting Kompany and refused to single the Belgian out for criticism.
"He started the game because he is the captain," the Chilean told reporters. "He made all the proof before the game, he said he was okay and the doctor said that, so I don't regret that.
"But I don't like to analyse individual performances with the media. I talk with the players and when we win or lose, it is the responsibility of the whole team."
Sunday's defeat saw City fall seven points behind the league leaders, but the former Malaga boss is convinced there will be more twists in the title race before the season is over.
"Of course it is possible Liverpool can drop points, or Chelsea, or our team also," he added.
"Any team can drop points every week. In the Premier League all the games are close and it's not easy to go and win."