Mourinho's side struggled for fluency in the opening 45 minutes at Craven Cottage, with the fatigue of a trip to Istanbul in the UEFA Champions League on Wednesday a possible explanation.
But they looked a team transformed in the second half with Andre Schurrle and Eden Hazard running rings around Fulham, the German scoring his first hat-trick for the club and Hazard stealing the show in midfield.
And Mourinho felt their improved performance was more down to the things he did not say during the interval.
He told Sky Sports News: "I didn't say a word at half-time, the first half was really bad for us. We said before they couldn't have more desire than us.
"In the second half we changed the intensity and started winning individual battles, it was much better.
"I decided not to speak at half-time because I would have needed more than 10 minutes, more than 20 minutes, but the players showed they are intelligent.
"It was silent [at half-time]. Normally I give them two or three minutes to clean or change boots or shirts. After that they know I'll start talking.
"Without words, they understand - especially if you know the person - what goes in their minds, so they knew the first half was really poor and they transformed it into a fantastic second half. I haven't had many first halves like this one - it was very bad.
"This was a real game of two halves. The first was very poor and the second was brilliant, it was a great three points for us."
Mourinho was delighted with Schurrle's goal haul, something he was well known for in the Bundesliga with Mainz and Bayer Leverkusen.
He only managed three goals in his first 19 Premier League outings, some of those off the bench, but doubled his tally with three composed finishes, two of them set up by Hazard.
"Schurrle's in a learning process in the Premier League but he's cool, he's a good finisher and that's what I expect from him," he added.
But Mourinho is not ready to describe his team as champions in waiting, despite taking a four-point lead over Arsenal, who went down 1-0 at Stoke, as the Portuguese coach feels their biggest threat comes from further north.
"We have four points more than Arsenal but if City win their two matches in hand they are top of the league," Mourinho said.
Mourinho also backed Fulham boss Felix Magath to turn the club's fortunes around. The German is yet to taste success with the Cottagers since taking over from Rene Meulensteen but Mourinho feels that will change soon.
He added: "I think Magath is the man for Fulham, he has experience and he has no fear. He has a lot to give to the players."