The former forward's coffin - draped in the club's famous colours - was transported through the city as part of a funeral cortege before being taken inside the stadium and placed in a position of honour in the centre circle of the pitch.
Supporters inside and outside the ground chanted the iconic attacker's name as his coffin was carried prior to his burial, due to take place to the north of the city following a special mass in a city church.
Eusebio, who died of heart complications at the weekend, played more than 300 games for the Portuguese giants during a glittering career, during which he famously lifted two European Cups and guided Portugal to a best-ever third-placed finish in World Cup 1966.
Around 10,000 supporters sang, waved flags and let off fireworks inside the stadium on Monday as Eusebio's coffin was taken to the centre circle and placed on a special golden plinth. Fans also draped scarves and shirts around the statue of the Mozambique-born legend, which stands outside the ground.
The footballing world took to social media on Sunday to pay tribute to Eusebio, with Cristiano Ronaldo describing his legacy as "always eternal" while former Seleccao star Luis Figo hailed him as "The king...the greatest."