CSKA midfielder Keisuke Honda and Inter Milan defender Yuto Nagatomo were among an otherwise full-strength Japan squad named by coach Alberto Zaccheroni on Monday for the November 14 game.
The Italian selected 13 Europe-based players in his 23-man party, although winger Ryo Miyaichi was once again overlooked as he continues to kick his heels on the bench at Wigan Athletic.
Playmaker Kagawa scored the winner as Japan stunned 1998 World Cup winners France 1-0 in Paris last month in a warm-up for their clash with Oman.
However, Zaccheroni was confident the Asian champions would cope in his absence.
"Kagawa and Honda have been regular features in my squads but they haven't always been available because of injuries," the Japan coach told reporters.
"But the players who have come in to deputise have all performed well. Kagawa is missing but I'm confident whoever plays will do a job."
Japan head to Muscat five points clear at the top of Group B in the final round of Asian qualifiers for the 2014 World Cup in Brazil. Victory would all but secure qualification.
Squad:
Goalkeepers: Eiji Kawashima (Standard Liege), Shusaku Nishikawa (Sanfrecce Hiroshima), Shuichi Gonda (FC Tokyo).
Defenders: Yuichi Komano (Jubilo Iwata), Yasuyuki Konno (Gamba Osaka), Yuzo Kurihara (Yokohama F-Marinos), Masahiko Inoha (Vissel Kobe), Yuto Nagatomo (Inter Milan), Atsuto Uchida (Schalke), Maya Yoshida (Southampton), Hiroki Sakai (Hannover).
Midfielders: Yasuhito Endo (Gamba Osaka), Kengo Nakamura (Kawasaki Frontale), Makoto Hasebe (Wolfsburg), Hajime Hosogai (Bayer Leverkusen), Keisuke Honda (CSKA Moscow), Hideto Takahashi (FC Tokyo).
Forwards: Ryoichi Maeda (Jubilo Iwata), Shinji Okazaki (Stuttgart), Mike Havenaar (Vitesse Arnhem), Takashi Inui (Eintracht Frankfurt), Hiroshi Kiyotake (Nuremberg), Takashi Usami (Hoffenheim).
