Kagawa demonstrated why he is being linked with a move to Manchester United during the off-season with a superb first goal in Japan's 2-0 friendly win over Azerbaijan on Wednesday.
Honda came through unscathed in his first Japan outing for nine months after recovering from injury while Arsenal's teenage winger Ryo Miyaichi has been selected after making his long-awaited international debut.
Asian champions Japan take on Oman on June 3 and Jordan on June 8 in Saitama before a difficult trip to Brisbane to tackle Australia four days later.
The Blue Samurai are also drawn alongside Iraq, led by former Japan coach Zico, in Group B.
Goalkeepers: Eiji Kawashima (Lierse), Shusaku Nishikawa (Shimizu), Shuichi Gonda (FC Tokyo)
Defenders: Yuichi Komano (Jubilo Iwata), Yasuyuki Konno (Gamba Osaka), Yuzo Kurihara (Yokohama), Masahiko Inoha (Kobe), Yuto Nagatomo (Inter Milan), Tomoaki Makino (Urawa), Atsuto Uchida (Schalke), Hiroki Sakai (Kashiwa), Maya Yoshida (Venlo)
Midfielders: Yasuhito Endo (Gamba Osaka), Kengo Nakamura (Kawasaki), Makoto Hasebe (Wolfsburg), Keisuke Honda (CSKA Moscow), Hajime Hosogai (Bayer Leverkusen), Hideto Takahashi (FC Tokyo)
Forwards: Ryoichi Maeda (Iwata), Shinji Okazaki (Stuttgart), Takayuki Morimoto (Novara), Shinji Kagawa (Borussia Dortmund), Ryo Miyaichi (Arsenal), Hiroshi Kiyotake (Cerezo Osaka), Mike Havenaar (Vitesse)