And Jose Mourinho also paid a moving tribute to his compatriot as he claimed the Eusebio's achievements would ensure he was never forgotten.
Nicknamed the Black Panther, Eusebio was regarded as one of the best players of all time and helped Portugal to third place at the 1966 World Cup, finishing as top scorer in the tournament with nine goals.
The Mozambique-born striker made his name at club level with Benfica, winning 11 league titles during a 15-year spell there and two Golden Boot awards as Europe's leading goalscorer.
He also notched 41 goals in 64 appearances for Portugal.
Manchester United and England great Charlton faced Eusebio in two of the greatest days of his own career, the 1966 World Cup semi-final, when England defeated Portugal at Wembley, and the 1968 European Cup final when United overcame Benfica in extra-time at the same venue.
The latter game is remembered for Eusebio applauding United goalkeeper Alex Stepney after a brilliant save that ensured the game went into the additional period, where United eventually won 4-1.
As ambassadors for their respective clubs, the pair crossed paths regularly.
"Without doubt, Eusebio was one of the finest players I ever had the privilege to play against," said Charlton.
"Not only that, he was a true sportsman, as he proved in applauding Alex Stepney for his save in the European Cup final.
"His goals record, for Benfica and overall, is incredible and stands the test of time.
"I met him on numerous occasions after our playing careers had finished and he always represented both his club and his country in exemplary fashion.
"I feel proud to have been both an opponent and friend and am saddened to hear of his passing."
Benfica were unable to confirm details of Eusebio's death, but reports in Portugal say he died of a cardiac arrest in the early hours of Sunday morning. He had been in poor health for some time and was hospitalised during Euro 2012 after suffering a heart scare in Poland.
Fans flocked to the Estadio da Luz and draped scarves on his statue at the ground in tribute.
Chelsea boss Mourinho said: "Eusebio is one of the greatest footballers in the history of football. He's at this level - Eusebio, Charlton, Pele.
"For Portugal he means more than that. No colour, no clubs, no political sides. For Portuguese people Eusebio is Eusebio and for sure you will get some images over the next couple of days and I think you will understand what Eusebio means for our country.
"I knew him since (I was) a kid. He played against my father. He played with my father in the national team. I met him when I was a kid. Our birthdays were separated by one day, his January 25, I'm January 26.
"He enjoyed his life, on the pitch, outside the pitch and I'm not so sad as I was in the morning because I think guys like him they never die. History is there and history doesn't let them die.
"I knew him well. He enjoyed his life. He leaves a great legacy. So rest in peace."