The Bernabeu legend hit out at the coach's negative tactics in Saturday's 1-1 draw with bitter rivals Barcelona, which effectively handed the title to the Catalans.
But Mourinho, who played four defenders and three defensive midfielders at home to the leaders, has shrugged off Di Stefano's comments - while careful not to insult a man who still carries significant power with the fans.
"He is one of the most significant people in the history of Real Madrid and I am nothing in the history of Real Madrid," Mourinho said ahead of the Copa del Rey final against Barca.
"But I am the coach and the coach is the one who decides.
"I am the coach. What do you want to do? It's me. The decisions are mine."