The pair came off the bench to inspire their side to a crucial victory at Craven Cottage on Saturday that moves them second in the Premier League standings
City went ahead with goals from Yaya Toure and Vincent Kompany before Kieran Richardson pulled one back for Rene Meulensteen's men. Kompany then netted a bizarre own goal to level an absorbin Premier League clash.
Navas came off the bench to restore City's lead 12 minutes from time and fellow substitute Milner made sure of the points five minutes later.
"It was a hard victory," said Pellegrini. "Fulham is not in a good position and they play an intensive game.
"Before they scored the first goal that was a counterattack, we had at least three clear chances to score goals.
"The second goal was bad luck. It's impossible to repeat it, but these things happen in football.
"At 2-0 I think we were playing well. At 2-2 I thought we had to change something.
"The creative players were tired. We had other options, players with a different style of play, and I had to change something.
"Navas and Milner made a huge contribution to the team with two goals."
Asked for his opinion on Kompany's own goal, Pellegrini joked: "Maybe he didn't remember that we changed sides.
"After you win, maybe you can laugh, but he was not happy."