Cristiano Ronaldo scored a hat-trick for the visitors while Karim Benzema also netted a fine acrobatic goal shortly after half-time.
"I liked my team a lot during 75 minutes. In the first 45 and then up until Ajax's goal [in the 56th minute] we had total control of the game against an Ajax team that were different from their usual version, much more defensive than usual," the 49-year-old told Canal+ after the match.
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The Ajax goal prompted a 15-minute period of dominance for the home side that Mourinho was glad to see end when Ronaldo scored his second and third goals.
"We lost a little control after Ajax scored, it became dangerous," he explained.
"Then we scored our third goal, Ajax understood that the game was over and we took control again."
When asked how he felt that his side had conceded another goal from a set piece the Madrid trainer said: "It's difficult to comment. I don't want to talk here, I want to talk inside the locker room."
On whether there were things he needed to fix with his side, he added: "That's your take, I don't think so. I think we were well organised."
Following reports that Cristiano Ronaldo is unhappy at the Bernabeu, Mourinho praised the forward's contribution as he scored a hat-trick for his side tonight.
"The team is achieving objectives. This win gives us a little calm. He [Ronaldo] knows his goals are important for the team," said Mourinho.
And when asked about the situation with Sergio Ramos following his spell on the bench, Mourinho said: "He's played and he's done well. My job is to get the best from the players.
"He's performed excellently in three matches after being on the bench. For me that's the important thing, it's what I'm looking for."
Madrid next face Barcelona in El Clasico on Sunday.