However, Pellegrini said it was a must to make so many changes as he has a number of key players injured at the moment and needs to think about the Premier League title chase, the Champions League and next weekend's Capital One Cup final.
"I think it's important for young players to play," Pellegrini said.
"They took their chance. I was very happy. Unfortunately, it's never good to lose 5-1, that's why I was not happy about the score, but I think there were many positive things for our young players.
"Maybe it's not the best thing to do all of them together but we had no choice as we had just 13 [fit] players. If there's one team that respects all the cups it's this team.
"That's why we're in the final of the Capital One Cup and won the previous two games in this competition. But I think this team has more important things at this moment."
He added: "I think we played the first half very well.
"It was a very tight game with both teams playing. Maybe Chelsea were the best team and we were playing with six young players but I was very happy.
"Unfortunately for us, in five minutes we threw away all the good work we'd done. At 3-1 it was very difficult. We created a few chances but also Chelsea scored more goals. Of course, as the game continues young players will tire because of the pace of the game."