The 31-year-old Honda, who plays for Mexican side Pachuca, last featured for the national team in September's World Cup qualifier against Saudi Arabia.
Augsburg attacking midfielder Takashi Usami, who is on loan at Fortuna Dusseldorf, and FC Tokyo midfielder Shoya Nakajima, on loan at Portuguese club Portimonense, were also named in Vahid Halilhodzic's squad.
Leicester forward Shinji Okazaki, who recently made a comeback from a knee injury, has been left out of the squad for the matches against Mali and Ukraine on March 23 and 27 respectively in the Belgian city of Liege.
Southampton defender Maya Yoshida (knee) and Borussia Dortmund midfielder Shinji Kagawa (ankle) have also been omitted because of injuries.
Halilhodzic had left out Kagawa, Okazaki and Honda for friendlies against Brazil and Belgium in November.
Japan will face Colombia, Senegal and Poland in Group H at this year's World Cup in Russia.
Squad:
Goalkeeper: Eiji Kawashima, Masaaki Higashiguchi, Kosuke Nakamura
Defenders: Yuto Nagatomo, Tomoaki Makino, Masato Morishige, Tomoya Ugajin, Hiroki Sakai, Shintaro Kurumaya, Gen Shoji, Wataru Endo, Naomichi Ueda
Midfielders: Makoto Hasebe, Hotaru Yamaguchi, Ryota Morioka, Gaku Shibasaki, Ryota Ohshima, Kento Misao
Forwards: Keisuke Honda, Yu Kobayashi, Yuya Osako, Genki Haraguchi, Takashi Usami, Kenyu Sugimoto, Yuya Kubo, Shoya Nakajima
(Reporting by Amlan Chakraborty in New Delhi; editing by Toby Davis)
