The Brazil international did not even make the bench as Andreas Christensen was handed a start, with rumours of a rift with Conte being the reason for his omission circulating around social media.
However, Conte insisted that the decision to go with Christensen was purely tactical, playing down suggestions of a breakdown in the pair's relationship.
“It's simple,” Conte said. “The coach has to make the best decision for the team, and tonight it was to play for Christensen and have (Ethan) Ampadu on the bench, good players for the present and future.
“I decided this tonight, maybe I can decide a different way in the future. It's normal. I have to make the best decision for the club, not for a single player. It was only a tactical decision. It's normal and this can happen to every one of my players.
“Christensen played an amazing game."
Chelsea, beaten 3-0 by Roma in their midweek Champions League fixture, produced an impressive performance against United on Sunday.
Alvaro Morata’s header was enough to secure a third straight league win that kept them only a point behind second-placed United and London rivals Tottenham Hotspur.
United pressed for an equaliser but the way champions Chelsea dug in to secure the three points impressed Conte.
“We must be pleased,” Conte added. “We played with great energy, passion and enthusiasm. There were a lot of positive things. The desire from my players, the fight and will to help each other.
"When we play in this way it's great. Last season we won the title and showed fantastic spirit in every game. This season, for many reasons, we started with a lot of problems. When you have problems you must pay attention because things can go down.
"To win against Manchester United gives you confidence."
(Reporting by Pete Hall, editing by Pritha Sarkar)
