Mourinho had said in January that being linked in the press with a return to former clubs Real Madrid and Inter Milan was a "tremendous honour". But already the club are moving to improve their squad as they look to close the gap on rivals Barcelona and Atletico.
The 21-year-old Militão, who moved to Porto from Brazilian side Sao Paulo last summer, has been in top form since arriving European football and has emerged the best defender in Portuguese topflight for the fourth time in February.
Militao has signed a six-year deal at the Bernabeu, with Madrid confirming he has committed his future to the club until 2025.
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Mourinho, who was sacked as Manchester United manager in December believes Zidane's second tenure with show people "how good he is", backing him to build on his treble UEFA Champions League and LaLiga successes. According to Marca, getting the deal done early was crucial as the estimated €50m clause was set to increase to €75m after 15th July.
Although naturally a centre-back, he has the technical ability necessary to also be successful at right-back and at defensive-midfield.
Militao has scored three goals for Porto this season, including one in the Champions League group-stage win over Schalke.