The Portuguese's effort meant City brought up their century of goals in 37 games, two more than it took last season.
Jesus added two second-half headers, capitalising on poor Fulham defending, for a side who have averaged five goals per game in home FA Cup matches under Guardiola.
Guardiola said: "After one or two minutes, I thought it would be a tough, tough game. They were incredibly aggressive up front. They are a team with a lot of courage but after the red card it was different. Even then they tried to play.
"Motivation was right. After 2-0, we missed a little bit some of the movements because they defended well and high.
"Hopefully in the next game against United, our fans can come and make the stadium full."