A knee injury forced Nagatomo to miss Japan's last qualifier in Jordan where the Asian champions needed only a point to claim an early place at the finals but lost 2-1 to the West Asians.
Australia's struggles in the five-team group mean Japan have a healthy six-point advantage with two games remaining as they attempt to book a fifth consecutive World Cup finals appearance with a top two finish.
They lead Group B on 13 points, with Jordan second on seven from six matches and Australia third with six points from five. Japan could qualify even in defeat if results in the group's other match on June 4 between Oman and Iraq go their way.
They will warm up for the match with a friendly against Bulgaria at Toyota on May 30 before the clash against the struggling Australians.
"The moment of truth has come for my team," coach Alberto Zaccheroni told Japanese reporters.
"We are a step away from qualifying for the World Cup. I don't want to start calculating how many points we need and what not, but just focus on winning these two games before us."
Playmaker Keisuke Honda was another recalled to the 26-man squad after missing the March match in Amman because of a knee injury but his chances of featuring against the Socceroos are hampered by his involvement in the Russian Cup final.
The CSKA Moscow attacker will only be able to join up with the squad the day before the Australia match with Stuttgart duo Shinji Okazaki and Gotoku Sakai also facing similar late arrivals in Japan because of German Cup duty.
"It'll be interesting to see what kind of shape they'll be in as they all arrive on different days," Zaccheroni said.
"Honda is getting better but he's not 100 percent. I'll ask the players coming back from Europe to take it easy for the first, two three days."
Zaccheroni has therefore handed first call ups to Kashiwa Reysol striker Masato Kudo and FC Tokyo midfielder Keigo Higashi.
Higashi was a member of Japan's Olympic team that reached the semi-finals in London last year, while Kudo has rattled in 13 goals in the J-League and Asian Champions League this season.
The 23-year-old striker is the latest candidate to fill the striker void for Japan ahead of the finals.
"What I can say about these two is that they are good utility players who can fill a number of positions and are constantly improving," Zaccheroni said.
"They are especially impressive when they get forward.
"But I want to make it clear that one call-up does not guarantee your place in the squad. You need to perform consistently at a high level, and let me remind everyone that I have picked new players before who have not made it back."