Kagawa received a blow to the chin in the 38th minute of his nation's 1-0 win over Jamaica, and although he managed to play on until his substitution in the 90th minute, the 25-year-old will not feature in Japan's meeting with Brazil on Tuesday but return to Dortmund instead.
The BVB star's departure leaves 1. FSV Mainz 05's Shinji Okazaki, Hertha Berlin's Hajime Hosogai and VfB Stuttgart's Gotoku Sakai as the remaining Bundesliga representatives in the Samurai Blues' squad.
Kagawa will join fellow midfielders Marco Reus and Ilkay Gündogan back in Dortmund, neither of whom went on international duty due to injury. The pair made tentative steps towards a recovery in a friendly yesterday.