The Chilean's side finished runner-up in Group D despite beating Champions League holder Bayern Munich 3-2 on Tuesday, but could have sealed top spot with one more goal.
City went into the game three points behind Pep Guardiola's side and fell behind to early goals from Thomas Muller and Mario Gotze.
However, the visitors recovered to secure a 3-2 win at the Allianz Arena, with James Milner scoring the winner to finish level on points with Bayern, but in second place in the group.
One more goal would have seen the visitors leapfrog Bayern and finish as group winners, with away goals between the sides deciding the final positions, however Pellegrini appeared to think his side needed to win 5-2 to finish top.
“I was tempted [to bring on Aguero] if we scored a fourth goal of course, that’s why I sent Aguero to warm up,” he told Sky Sports. "But I think it was a risk to continue with David Silva, he could not play more than 70 minutes. It was important to be top of group but not the most important thing.
“It’s very difficult to score two [more] goals.”
The Chilean also admitted he was delighted to have triumphed over Guardiola’s side to make amends for being beaten by the Champions League holders at the start of the season.
"We wanted revenge for the first game [which Bayern won 3-1] and to show it was not that different between Bayern and our team,” he added.
"To win here and score three goals without Vincent Kompany, Yaya Toure, Alvaro Negredo and Sergio Aguero shows we have a very good squad also, so it's a very important victory."