The 84-year-old Di Stefano, who won five consecutive European Cups with Real between 1956 and 1960, made scathing remarks about Mourinho's strategy of instructing his players to sit back against Barcelona in Saturday's 1-1 La Liga draw at the Bernabeu and try to catch the league leaders on the break.
"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 at Valencia's Mestalla stadium where Wednesday's Kings Cup final with Barca will be played.
"But I am the coach and the coach is the one who decides.
"I am the coach," he repeated. "What do you want to do? It's me. The decisions are mine."
In his Monday newspaper column, Di Stefano described Barca as a lion toying with a mouse and called for different tactics in Wednesday's final, the second game in a four-match sequence of "Clasico" confrontations to be played over 18 days.
"Saturday's game should give pause for thought on how to face up to the next because trying to play Barcelona on the break clearly isn't the most adequate," Di Stefano wrote.
"Barca treat the ball with respect, adoration, they almost pamper it. To watch this team in action is a delight.
"Barca play football and dance, Real just dashed from here to there constantly. It's clear that Barcelona are superior. Real were a team without personality."
Di Stefano's criticism of Real's playing style and his florid praise for their arch rivals carries extra weight given his celebrated status within the club.
However, Mourinho gave no indication he was about to change tack and deploy a more attacking formation on Wednesday.
Gone were the days when Real had six players doing all the work at the back and four forwards who were not expected to muck in and help defend, the Portuguese said.
"I know that this will be a problem for many of you," he said. "But I think that the fans, although they are not professionals, are opening their eyes little by little and that's why they'll be behind their team tomorrow."
Barca and Real also meet in the semi-finals of the Champions League, with the first leg at the Bernabeu in Madrid on April 27 and the second leg at the Nou Camp in Barcelona on May 3.