The 35-year-old midfielder, who skippered Gamba Osaka to a domestic treble last year, has won 152 caps for his country but was the glaring omission from the 31-man squad named on Thursday by Halilhodzic, who took charge earlier this month.
The former Asian Player of the Year has been a central figure in the Japanese midfielder for over a decade, going to three World Cups and setting up numerous goals with his threaded through balls and pinpoint free-kicks.
He was also initially sidelined by Halilhodzic's predecessor, Javier Aguirre, but the Mexican brought back the wily campaigner for the Asian Cup only to see the holders go out surprisingly to United Arab Emirates in the quarter-finals.
But the new head coach opted to look elsewhere, casting the net far and wide by also selecting 12 backup players for the matches against Tunisia in Oita on March 27 and Uzbekistan four days later in Tokyo.
Injured fullbacks Atsuto Uchida and Yuto Nagatomo were also called up as the former Algeria and Ivory Coast boss attempts to view as many players as possible before the World Cup qualifying campaign starts in June.
Endo's uncapped Gamba team mates Takashi Usami and Hiroki Fujihara were included by Halilhodzic alongside regulars Makoto Hasebe, Shinji Kagawa, Keisuke Honda and Shinji Okazaki.
Squad
Goalkeepers: Eiji Kawashima (Standard Liege), Masaaki Higashiguchi, (Gamba Osaka), Shusaku Nishikawa (Urawa Red Diamonds), Shuichi Gonda (Tokyo), *Akihiro Hayashi (Sagan Tosu)
Defenders: Hiroki Mizumoto (Sanfrecce Hiroshima), Yuto Nagatomo (Inter Milan), Tomoaki Makino (Urawa Red Diamonds), Masato Morishige (Tokyo), Kosuke Ota (Tokyo), Atsuto Uchida (Schalke 04), Maya Yoshida (Southampton) Hiroki Fujiharu (Gamba Osaka), Hiroki Sakai (Hannover 96), Gotoku Sakai (VfB Stuttgart), Gen Shoji (Kashima Antlers), *Kazuhiko Chiba (Sanfrecce Hiroshima), *Tsukasa Shiotani (Sanfrecce Hiroshima), *Daisuke Suzuki (Kashiwa Reysol), *Shintaro Kurumaya (Kawasaki Frontale)
Midfielders: Yasuyuki Konno (Gamba Osaka), Makoto Hasebe (Eintracht Frankfurt), Toshihiro Aoyama (Sanfrecce Hiroshima), Shinji Kagawa (Borussia Dortmund), Hiroshi Kiyotake (Hannover 96), Hotaru Yamaguchi (Cerezo Osaka), Gaku Shibasaki (Kashima Antlers), *Yojiro Takahagi (Western Sydney Wanderers) *TakujiYonemoto (Tokyo), *Shogo Taniguchi (Kawasaki Frontale) *Kotaro Omori (Gamba Osaka)
Forwards: Shinji Okazaki (Mainz 05), Keisuke Honda (AC Milan), Shinzo Koroki (Urawa Red Diamonds), Yu Kobayashi (Kawasaki Frontale), Takashi Inui (Eintracht Frankfurt), Kensuke Nagai (Nagoya Grampus), Yuya Osako (Cologne), Takashi Usami (Gamba Osaka), Yoshinori Muto (Tokyo), *Yohei Toyoda (Sagan Tosu), *Kengo Kawamata (Nagoya Grampus), *Yoichiro Kakitani (FC Basel)
*Denotes backup
(Writing by Patrick Johnston in Singapore; Editing by John O'Brien)
