The winger rounded the Japanese goalkeeper to net after just 18 minutes to give Brazil the lead.
The Brazil captain bagged his second just two minutes after half-time.
Neymar netted his hat-trick after 77 minutes when he scored a rebound after the Japanese keeper parried a shot from Coutinho.
The Barcelona striker grabbed his and Brazil’s fourth with an 81st-minute header.
BRAZIL XI: Jefferson, Danilo, Miranda, Gil, Filipe Luís, Luiz Gustavo, Elias, Willian, Oscar, Diego Tardelli, Neymar
Subs: Cabral, Grohe, David Luiz, Jesus, Gil, Dodo, Fernandes, Romulo, Souza, Everton Ribeiro, Kaka, Coutinho, Robinho
JAPAN XI: Kawashima, Ota, Sakai, Shiotani, Morishige, Tanaka, Taguchi, Morioka, Shibasaki, Okazaki, Kobayashi
Subs: Nishikawa, Gonda, Mizumoto, Nagatomo, Suzuki, Nishi, Kagawa, Hosogai, Honda, Kakitani, Muto, Havenaar