But the coach had to drop another key full-back, Schalke's Atsuto Uchida, due to a fresh injury while star playmaker, CSKA Moscow's Keisuke Honda, remains sidelined having missed the two previous qualifiers with a knee injury.
"Of course, Honda is an important player. But we didn't even have Nagatomo against North Korea and Uzbekistan. We will manage to find a good balance," Zaccheroni said. "It is my job to get the best out of the players available."
Without Honda, who powered Japan to the Round of 16 at last year's FIFA World Cup and a record fourth AFC Asian Cup title in January, the Blue Samurai have lacked inspiration - beating Korea DPR 1-0 and drawing with Uzbekistan 1-1 away.
Zaccheroni's latest 23-strong squad for the 11 October tie was otherwise devoid of surprises and included ten European-based players. The side will warm up with a home friendly against Vietnam on 7 October.
"I am very satisfied with our performances in the last three games. Nagatomo missed all the three matches but the players that came in did a good job," Zaccheroni added.
Nagatomo suffered a dislocated right shoulder at the end of July in Inter's pre-season friendly against Celtic in Dublin. Honda is recovering from surgery on his right knee and Uchida strained thigh muscles in training on Tuesday.
Tajikistan have lost both of their Group C qualifiers 1-0, to Uzbekistan and Korea DPR. Japan and Uzbekistan are level on four points in the group, followed by Korea DPR with three.
Goalkeepers: Eiji Kawashima (Lierse SK/BEL), Shusaku Nishikawa (Sanfrecce Hiroshima), Shuichi Gonda (FC Tokyo)
Defenders: Yuichi Komano (Jubilo Iwata), Yasuyuki Konno (FC Tokyo), Yuzo Kurihara (Yokohama F Marinos), Masahiko Inoha (Hajduk Split/CRO), Yuto Nagatomo (Inter Milan/ITA), Tomoaki Makino (FC Cologne/GER), Maya Yoshida (VVV Venlo/NED)
Midfielders: Yasuhito Endo (Gamba Osaka), Kengo Nakamura (Kawasaki Frontale), Yuki Abe (Leicester City/ENG), Makoto Hasebe (Wolfsburg/GER), Chikashi Masuda (Kashima Antlers), Hajime Hosogai (Augsburg/GER)
Forwards: Jungo Fujimoto (Nagoya Grampus), Tadanari Lee (Sanfrecce Hiroshima), Shinji Okazaki (Stuttgart/GER), Mike Havenaar (Ventforet Kofu), Shinji Kagawa (Borussia Dortmund/GER), Hiroshi Kiyotake (Cerezo Osaka), Genki Haraguchi (Urawa Reds)