Academy prospects Antonio Adan, Nacho, Jose Rodriguez and Alvaro Morata were all given a run out in the final game of the Champions League group stages, but it was the more established stars that shone as goals from Cristiano Ronaldo, Kaka and a brace from Jose Maria Callejon handed Real their sixth victory over the Dutch side in the past three seasons.
Mourinho said: "Nacho has played because (Alvaro) Arbeloa is suspended and he is a player of the first team.
"He is a kid with a strong personality and we knew he would have no problem. He had a fantastic mentality and committed no defensive errors.
"We like Jose a lot too, although he has not played a lot with the Castilla. He is only 17 years old but you could imagine he is 20 and he has the level to play at Real Madrid.
"Morata is also a first-team player but he has (Karim) Benzema and (Gonzalo) Higuain in front of him. Every minute he plays is good for him but one game doesn't change my thinking.
"Someone like Callejon is always in my mind because he always plays well and leaves everything on the field."
Mourinho was also not flustered at only finishing second in Group D and insisted that just qualifying from the "group of death" was an achievement in itself.
"We have to respect everyone, but when you finish first you believe you deserve an easier rival," he added. "We will face a first-placed team and it will be a difficult opponent but we will see in February.
"Three seasons in a row we have qualified before the final match. This year in the group of death we have collected 11 points and if it hadn't been for what happened in Manchester we would have two more. We have had problems with injuries to important players but we have qualified well due to our work."
Ajax boss Frank de Boer accepted he was happy just to have European football to look forward to next year as his side finished third in the group, and they now have the chance to win the Europa League in their own stadium in May.
He said: "At the start of the group it is almost impossible not only to qualify for the Champions League but also the Europa League so we are very proud to finish third.
"We have a chance to go to the final of the Europa League in our own stadium but it will be very difficult as there are many good teams in that competition and we still have to improve a lot."
The former Holland international admitted he was far from happy with his side's performance in the first half but he was satisfied with their reaction after the break as Derk Boerrigter pulled a goal back.
The visitors could even have had more as Danny Hoesen missed a glorious chance to make it 3-2.
He added: "We are a very young team and when you come to a place like the Bernabeu it can be hard even with everyone at their best, so when you have eight players below that level it is impossible.
"I made that clear at half-time and, although there are goals like the third one which are impossible to stop, we managed to slow Madrid down a lot and create our own chances.
"Unfortunately we couldn't get it to 3-2 and then when they scored the fourth it was over."