City travel to Spain for the second leg of their semi-final against Madrid on Wednesday and Pellegrini indicated his unhappiness at the scheduling of the Southampton game for a late kick-off on Sunday, instead of Saturday.
"I would do exactly the same again because we have an important game on Wednesday, that we play now for the final in the Champions League," said Pellegrini, who rested Sergio Aguero, Vincent Kompany and Kevin de Bruyne on Sunday.
"Maybe if we played on Saturday we could have another option for this game but playing with too many players that are not playing often is difficult.
"I tried to select a team that would win the game. I also had to select a team based on who would play on Wednesday."
Pellegrini hoped the heavy defeat would not hurt his team's chances in Madrid and insisted City were still in a good position to seal Champions League qualification by finishing fourth in the Premier League.
"The best way to prepare is to win but we couldn't do it," he added. "I expected more -- especially defending. I'm very frustrated because I didn't expect that performance.
"(Now) it all depends on what we can do in these last two games. We are three points behind Arsenal and if we beat Arsenal we'll be in third position before the last game."
(Reporting by Simon Jennings in Bengaluru; editing by Sudipto Ganguly)
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