City came from a goal down to eventually win 3-2 on Saturday.
"He is not a guy who scores normally," Guardiola said.
"They defended with five at the back after we started really well. In two minutes we had two chances.
"When they defend five there is one man free on the edge of the box and that is Kovacic. Jimenez has to defend Kovacic but then there are no transitions.
"The two goals today in that position were because they could not defend it. The first goal was brilliant, the second as well.
"We have to exploit more against teams that play five at the back. Kova was really important. Now the opponents know they cannot leave him alone, otherwise he can score a goal."
City's manager admits he was impressed by Fulham on the day.
"My feeling is the game was well played," he said.
"Adama (Traore) is unstoppable, that guy. Not any player can control when he had the ball. In the first two touches he is going to run and it’s impossible to control him.
"In the first half I think it was well played but for one or two transitions. I always had that feeling that they had chances but it was well played.
"We scored the third and we felt we were going to control but in that moment we didn’t know what was going to happen. A fantastic goal from Jeremy (Doku).
"They put a lot of runners and had a lot of the ball. After it happened it was a tough game but we knew it.
"We talked with the team and said today would be a tough game after a long week and they have lost just one game at Old Trafford. The rest they had incredible results.
"Many years Marco (Silva) has been an exceptional manager and he is getting better. We have to deal with that. When we have an incredible run of not losing in Etihad we have won some in that way. Nothing in life is easy."
