Kubo, who scored in Japan's previous two qualifiers, joined Leicester City's Shinji Okazaki and AC Milan's Keisuke Honda in the forward line for the June 7 match against Syria in Tokyo and the away match in neutral Tehran six days later.
More surprising was the selection of Beroe Stara Zagora's 27-year-old midfielder Kato.
"Some of you may not know much about him but I have been tracking him for one year," Halilhodzic was quoted as saying by the Kyodo news agency.
"I have watched him play four matches in Bulgaria and have also watched video footage of him a number of times. He is aggressive and knows how to win the ball."
"He is a similar player to (Cerezo Osaka midfielder) Hotaru (Yamaguchi), although not as powerful, and he is a good passer of the ball," the Bosnian added.
"I am not planning on playing him straight away but this gives me a chance to take a look at him and see what's what."
Halilhodzic dropped Reds goalkeeper Shusaku Nishikawa, along with FC Tokyo centre back Masato Morishige and Cerezo's Hiroshi Kiyotake, and brought back Rio Olympic keeper Kosuke Nakamura.
"This doesn't mean they are axed for good. It simply comes down to some players playing better than other players. The players in the best form have the right to be picked," Halilhodzic said.
Squad:
Goalkeepers: Eiji Kawashima, Masaaki Higashiguchi, Kosuke Nakamura
Defenders: Yuto Nagatomo, Tomoaki Makino, Tomoya Ugajin, Maya Yoshida, Hiroki Sakai, Gotoku Sakai, Gen Shoji, Genta Miura
Midfielders: Yasuyuki Konno, Shu Kurata, Shinji Kagawa, Kohei Kato, Hotaru Yamaguchi, Wataru Endo, Yosuke Ideguchi
Forwards: Shinji Okazaki, Keisuke Honda, Takashi Inui, Yuya Osako, Genki Haraguchi, Yuya Kubo, Takuma Asano
(Reporting by Amlan Chakraborty in New Delhi; Editing by John O'Brien)
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