The Premier League side recovered from a poor start at the Allianz Arena on Tuesday, as German and European champions Bayern Munich raced into a 2-0 lead after just 12 minutes.
Goals from David Silva, Aleksandar Kolarov and James Milner ultimately gave City a come-from-behind 3-2 win, but Pellegrini could yet rue his failure to push on for a fourth - apparently misunderstanding that City needed just a single goal to climb to the summit.
Both teams had already qualified for the last 16 but had City registered a 4-2 scoreline, as they almost did through substitute Alvaro Negredo late on, they would have topped the table by virtue of a superior head-to-head record - bettering Bayern's 3-1 win at the Etihad Stadium in October.
With one eye on Saturday's crucial Premier League clash with Arsenal, Pellegrini rested a number of key first-teamers, with captain Vincent Kompany, Negredo and his strike partner Sergio Aguero all named among the substitutes.
After the match, Pellegrini was asked whether he considered bringing Aguero on to chase top place in the group and suggested that a fourth goal would have seen the Argentina international introduced - before focusing on the need to withdraw the excellent Silva after 70 minutes of the playmaker's return from a calf injury.
Instead, at 3-2, midfielder Jack Rodwell was brought on for striker Edin Dzeko as the visitors shut up shop.
"I was tempted (to bring Aguero on) if we scored a fourth goal, that's why I sent Aguero to warm up," Pellegrini told Sky Sports.
"Also, I think it was a risk to continue with Silva, for him to play more than 70 minutes.
"I repeat for our team it is very important to be the first in the group, but not the most important thing.
"It was difficult to score two (more) goals and I think that Silva, after being out, could not play more than 70 minutes."
The confusion somewhat unfairly took the focus off a sensational comeback that prevented Bayern from become only the sixth team in Champions League history to progress from the group stages with a 100 per cent record - something that appeared a formality after early goals from Thomas Muller and Mario Gotze.
City, who suffered the ignominy of failing to win a single match in last season's competition, reduced the arrears through Silva before Kolarov's penalty levelled matters with 59 minutes played.
Milner was brought down by Dante for the spot kick, having claimed the assist for Silva's close-range effort, and he completed a superb individual display by clinically dispatching Jesus Navas' cross to seal the points.
"I think it says a lot about the dressing room and the players we have and the character we have," Milner added.
"It was a terrible start from us, sloppy goals, and they looked like they were going to walk away with it.
"To come to a place like this, go two down against that sort of side and come back and win shows how much character there is in the dressing room.”
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