They had been called up for World Cup qualifiers but didn't travel after Premier League teams had objected to their players going to South American nations, which are on the UK's Covid red list.
Brazil started the day at the top of the standings in Group D, which includes Germany and Ivory Coast, but needed a win or draw to advance.
Richarlison said after Brazil's 1-0 win against Chile in the Copa America quarterfinals that his club Everton had allowed him to play in Japan.
It was the Selecao's ninth consecutive victory, and another display that suggests the tournament hosts are the favorites to defend their South American title.
Tite tested Everton Ribeiro and Gabriel Barbosa up front at practice on Tuesday instead of Lucas Paquetá, Richarlison and Gabriel Jesus, who started in Brazil's 3-0 win over Venezuela.
Gabriel Jesus, Roberto Firmino, Richarlison and Gabriel Barbosa are in contention.
Richarlison opened the scoring in the 65th minute on Friday at the Beira-Rio stadium in Porto Alegre and Neymar added the second from the spot in added time.