Yaya Toure scored a hat-trick as City eased past the struggling Cottagers at the Etihad Stadium to climb to third in the Barclays Premier League.
Fernandinho and Martin Demichelis also got on the scoresheet as bottom side Fulham capitulated after the sending-off of Fernando Amorebieta early in the second half.
The goals scored were a fine riposte to top two Chelsea and Liverpool - who both scored six goals on the same day - but Pellegrini was almost as pleased not to concede.
The Chilean said: "It was a complete performance because we kept a clean sheet again. For me that is important.
"In the last part of the season I think we must be a very balanced team - not only scoring five goals but it is important not to concede goals.
"We scored five goals and we had a lot more chances.
"It is true that with only 10 players it was more difficult for Fulham, but before the player was sent off we scored two goals and had two or three more clear chances."
Toure's first two goals were penalties, both conceded by Amorebieta, the second of which brought about his dismissal.
He then curled in a sublime third from long range to take his tally for the season to 20.
The Ivorian is the third City player to reach that landmark this season after Sergio Aguero and Alvaro Negredo while Edin Dzeko, who missed the game through illness, has 18.
Pellegrini said: "I think it is important for Yaya, the way he plays.
"Maybe at the beginning of the season he received some criticism that he was not defending well, but defending is not allowing him to play freer.
"He is a very important player playing the way he likes to play. Scoring 20 goals for a midfielder is not easy in a season."
The victory puts City in good heart for their derby against Manchester United on Tuesday and another difficult trip to Arsenal next weekend.
Pellegrini said: "Always winning is good preparation for the next match.
"Winning today the way we did, scoring five goals and not conceding, it is always important but the derby is a special match, so we must try to forget about what we did today and start thinking about what we must do against Manchester United."
The defeat left Fulham bottom of the table and manager Felix Magath was not happy with the way his side were overrun in the final half-hour.
But with the five teams immediately above them also failing to pick up points, the German felt the result was not too damaging.
Magath said: "Nobody expected a win here at Man City, so if we lost it is normal. Nobody will care about it.
"But I am not happy with our performance after the second goal. Sure, it was a bad moment for us and we lost a player but that is no reason to stop playing.
"I think we have to play for 90 minutes here with 10 or 11 players. It doesn't matter."
Fulham have seven games remaining to save their top-flight status, starting with next week's home clash against Everton.
Magath said: "That we lost today is not a problem. We have to win our home games and that is important for us.
"We can look forward to next week but we have to talk about this situation, that we don't fight to the end of the game.
"It is not correct, especially for our fans. They came to Manchester, like us, to win and make a good game.
"We have to fight for 90 minutes and not only 60."