City picked up three points with a hard-fought 3-2 win over the Cottagers with the Croatian striking twice before a fantastic third from Jeremy Doku.
The boss said that Fulham switched to five at the back after we created two good chances in the opening minutes to make less space for the forwards.
That left Kovacic as the spare man on the edge of the box to score a deflected equaliser before a well-taken second after the break.
Fulham had a number of chances with Ederson pulling off a big save from Adama Traore, but Guardiola felt the system worked well to give us the edge in a hard game.
“My feeling is the game was well played,” he said after the match. “Adama 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. [It was] a fantastic goal from Jeremy.
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“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 [was going to be].
“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.”
Kovacic was the man of the match after his goals, adding to his opening day strike in the win over Chelsea.
And Guardiola says the Croatian has also been a big player, even if the spotlight only falls on him after hitting the back of the net.
“Maybe it happens when he scores two goals,” the boss added. “He is not a guy who scores normally.
“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.”
