Varane was selected ahead of Sergio Ramos for the Champions League win.
Mourinho complained: "Why isn't anyone talking about Varane when a week ago people were talking about his depression and frustration? At 19 he's been given the responsibility of playing a match of maximum importance and he's done a fantastic job.
"Now no one's talking about Varane. There's a tendency to talk about those that don't play. Every decision that I take is deliberated and you have your reasons and justifications for your options. It's curious that people always speak about those that don't play and not those that do."