Regarded as one of the greatest footballers of all time, the player known as the "Black Panther", died after suffering cardio-pulmonary arrest early on Sunday morning.
He had been hospitalised several times in recent years with various health problems and suffered a stroke in June 2012.
"Eusebio showed signs of fragility lately, but I didn't expect this at all," said Joao Malheiro, author of the player's biography Eusebio - my story.
The player's remains will be taken to the Luz stadium in Lisbon where fans at his former club, Benfica, can pay their final respects.
The Portuguese government also decreed three days of national mourning, with flags in Lisbon to fly at half-mast.
The Portuguese Football Federation said there would be a minute's silence ahead of Sunday's Portuguese Cup games, as tributes flowed in for the player.
FIFA president Sepp Blatter wrote on Twitter that "Football has lost a legend", while current Portugal captain Ronaldo wrote: "Always eternal #Eusebio, rest in peace."
The Mozambique-born striker made his name at Benfica, winning 11 league titles and one European Cup during a 15-year spell there. He also won two Golden Boot awards as Europe's leading goalscorer.
In addition to his 11 league titles, Eusebio won five Portuguese cups in his 15 years at Benfica and was Portugal's top league scorer between 1964 and 1973.
He scored 733 times in 745 professional matches.
Despite his scoring record, however, his only appearance at a World Cup finals was in 1966 in England.
He helped Portugal however take third place in the tournament, where he was top scorer with nine goals. In total, he scored 41 goals in 64 appearances for Portugal.
Alex Stepney, the former Manchester United goalkeeper, who famously saved a late shot from Eusebio during the 1968 European Cup final at Wembley paid tribute.
"I made the save and out of the corner of my eye I saw him still standing in front of me. It was only afterwards that I saw what he had done. The fact he was standing there clapping before running away is a mark of the man," Stepney said.