Eusebio, 70, was admitted to Lisbon's Luz hospital after arriving on a medical flight on Wednesday.
"The tests conclude that on the 24th of June he had a cerebrovascular accident," Luz hospital clinical director Jose Roquette said in a statement emailed to Reuters.
Eusebio is in a stable condition and has been moved out of intensive care.
"Eusebio is conscious, lucid and collaborates in all the medical care being done. His family is with him and his friends have been visiting," Roquette said.
"He will stay in hospital for an undetermined period of time and constantly under watch."
Eusebio, Portugal's football ambassador, has been admitted to hospital four times since December. He has been suffering from hypertension and his doctors have said he must have regular examinations.
Eusebio travelled with the national team to Poland and was in the stands for the quarter-final win over the Czech Republic, cheering alongside former Portugal captain Luis Figo.
Nicknamed the 'black panther', Eusebio grabbed international headlines during the 1966 World Cup in England when Portugal finished third. He also helped his Portuguese club side Benfica reach four European Cup finals in the 1960s.