Interestingly, there were both jeers of disappointment at seeing the £198 million (S$344 million) man come off, as well as cheers when the Liverpool fans among the 20,385-strong crowd realised that Philippe Coutinho was the replacement.
Amid a more boisterous atmosphere than Thursday night's muted affair, Neymar started in a deeper central midfield role behind the front three of Gabriel Jesus, Roberto Firmino and Everton as Brazil coach Tite made just two changes to the side that were held 1-1 by Senegal at the same venue last Thursday.
But Neymar's exit seemed to unsettle the world No. 3 Brazilians, who were trying to end a run of three games without a win.
The young Nigerian side, whose average age is 23.5 years, gradually imposed themselves in the game as the Selecao struggled to cope with their rivals' pace and power.
Leicester City defensive midfielder Wilfred Ndidi was a beast in the engine room as he easily outmuscled the likes of Coutinho, even decking the Bayern Munich man in the 27th minute.
Skipper Dani Alves' cross from the right was headed on to the bar by Marquinhos, and Casemiro was on hand to sweep home the loose ball.
Brazil then peppered their African opponents' goal with shots as substitute Richarlison struck the woodwork twice, while both Nigeria goalkeepers - Francis Uzoho and debutant Maduka Okoye - also made crucial stops to deny the Selecao.
The five-time world champions knew it was not to be their night when Coutinho's goal-bound shot was miscleared by Semi Ajayi on the line and into the grateful arms of Okoye in the 86th minute.
Samuel Chukwueze then fired straight at Ederson from a tight angle in the next minute, but world No. 34 Nigeria will be pleased with their first draw against Brazil after a 3-0 defeat in 2003.