Kagawa completed the full 90 minutes in the competition's Group A curtain-raiser at the newly-built Estadio Nacional Mane Garrincha in Brasilia. It was the first international match to use goal-line technology, but it was not needed for any decisions.
Brazil took the lead after just three minutes thanks to a stunning 20-yard strike from Barcelona's summer signing Neymar.
Japan weren't about to let the early strike derail them, but while they passed the ball well and enjoyed some good possession, there was a lack of penetration in the final third.
Hulk and Fred each went close to doubling Brazil's advantage as the half went on, before Paulinho made it 2-0 three minutes after the restart. It was a fine strike from the Brazilian who controlled Dani Alves' cross and hammered a low shot past Japan stopper Eiji Kawashima.
Substitute Jo, formerly of Manchester City, made sure of the victory in injury-time, scoring with his first touch after being set up brilliantly by Oscar.
The second game in Group A between Javier Hernandez's Mexico and Italy takes place on Sunday, KO 20:00 BST.