The match was held at Tokyo's National Stadium on Monday, where Brazil defeated the host 1-0.
Neymar's penalty 13 minutes from time earned Brazil a win over fellow World Cup qualifier Japan.
Substitute Richarlison was brought down by Endo and referee Alireza Faghani pointed to the spot.
Faghani prepares to officiate in the 2022 World Cup. He has previously officiated at the 2014 and 2018 FIFA World Cup.