The Argentine striker came off after 64 minutes but that was always the plan, according to the City boss.
City got back to winning ways thanks to goals from Kevin De Bruyne, Fabian Delph and Aleksandar Kolarov and Pellegrini called it an “important reaction”.
Manuel said: “It was not an easy week - we’ve won just one point of our last six so it was important to beat a difficult team who were unbeaten away.
“Kun came off as a precaution. I spoke with him before the game and we said he would play 65 minutes. He has a kick in his heel, but nothing important.
“He has played three games in a row and that’s why he came off – it’s important to see with the medical staff how he recovers from this game.
“I was very pleased with the team’s reaction. We were a little nervous until the third goal, but I’m happy with the performance and the result.
“We must try to recover the players for Tuesday. It’s important for us to reach the semi-final of the League Cup.”
City have lost two home games at the Etihad Stadium so far this season which is too many according to their manager.
In his post-match press conference, Pellegrini outlined home form as key to his side’s chances of mounting a serious title challenge this season.
“If you want to be involved in the title race you cannot drop more points at home,” he declared.
“We’ve lost already six points against Liverpool and West Ham. It’s not easy playing so many games with the same players but I think the start was really important.
“We played on Wednesday a very difficult game and we didn’t have 72 hours to recover from that game – Southampton had the whole week.
“The third goal of Alex fortunately killed the game for us - maybe we didn’t have a good week but we continue in the Champions League, the Capital One Cup and the Premier League.
“It’s not a crisis – it’s a very good season.”
