The Manchester United and Milan stars will be at the forefront of Alberto Zaccheroni's squad while Southampton's Maya Yoshida will also be on the plane to Brazil
The attacking duo will provide the creative flair for the Asia Cup holders while Southampton's Maya Yoshida will help add defensive steel.
Zaccheroni, coach of Japan since August 2010, selected 12 players based in Europe and 11 from the J-League as the Italian prepares to lead Asia's top-ranked nation to Brazil.
Milan's Honda and Manchester United's Kagawa will be critical to Japan's hopes of progressing from Group C, where they will face Cote d'Ivoire, Greece and Colombia.
Japan traditionally struggle to produce top-line strikers and Zaccheroni will most likely rely on Honda and Kagawa to both create and score most of the team's goals at the World Cup.
Underlining Japan's struggles up front was the one surprise selection in Zaccheroni's squad, with Yoshito Okubo of Kawasaki Frontale named despite having only been picked once before during the Italian's tenure.
Okubo was the leading goal-scorer in the 2013 J-League season, as he helped Kawasaki to a third-placed finish.
With 54 caps and five international goals to his name, the 31-year-old Okubo will challenge the likes of Mainz striker Shinji Okazaki and 1860 Munich's Yuya Osako for a spot up front.
Japan will start their World Cup campaign against Ivory Coast on June 14 in Recife, before taking on Greece in Natal five days later and Colombia in Cuiaba on June 24.
Squad in full:
Goalkeepeers: Shuichi Gonda (Tokyo), Eiji Kawashima (Standard Liege), Shusaku Nishikawa (Urawa Reds)
Defenders: Masahiko Inoha (Jubilo Iwata), Yasuyuki Konno (Gamba Osaka), Masato Morishige (Tokyo), Yuto Nagatomo (Inter), Gotoku Sakai (Stuttgart), Hiroki Sakai (Hannover), Atsuto Uchida (Schalke), Maya Yoshida (Southampton)
Midfielders: Toshihiro Aoyama (Sanfrecce Hiroshima), Yasuhito Endo (Gamba Osaka), Makoto Hasebe (Nuremberg), Keisuke Honda (Milan), Shinji Kagawa (Manchester United), Yoichiro Kakitani (Cerezo Osaka), Hiroshi Kiyotake (Nuremberg), Manabu Saito (Yokohama F Marinos), Hotaru Yamaguchi (Cerezo Osaka)
Forwards: Shinji Okazaki (Mainz), Yoshito Okubo (Kawasaki Frontale), Yuya Osako (1860 Munich)