The Bosnian took a gamble by leaving Keisuke Honda, Shinji Okazaki and Shinji Kagawa on the bench but the experienced trio were not required as Takuma Asano and 21-year-old Yosuke Ideguchi sealed his team's place at the 2018 finals in Russia.
The win means Japan will finish top of Group B in Asia's qualifying tournament while the Australians need to defeat bottom side Thailand on Tuesday and hope Saudi Arabia do not beat the Japanese to guarantee an automatic slot.
"We faced a lot of difficulties and challenges but the players played like heroes against a high-quality team and this should be the standard (we aspire to)," Halilhodzic was quoted as saying by Kyodo News.
"I thought that I should put my faith in younger players and I showed that that was the correct call and it is a good thing for Japanese soccer.
"I want to dedicate this win to the people of Japan and I think they are proud of the players."
Asano put the hosts in front four minutes before halftime when he beat the offside trap to steer Yuto Nagatomo's inswinging cross from the left beyond goalkeeper Maty Ryan.
Eight minutes from time Ideguchi sealed the win with a fine long-range strike that flew into the top corner of Ryan's net.
MISSED CHANCE
South Korea missed a chance to secure a place at the finals when Shin Tae-yong's side were held to a 0-0 draw by already-qualified Iran, who played much of the second half with 10 men after Saeid Ezatolahi's sending off in the 52nd minute.
The draw coupled with a 3-1 win for Syria over Qatar and China's 1-0 victory over Uzbekistan means the battle for second and third place in Group A remains in the balance.
South Korea stay second but Syria, thanks to a double from Omar Kharbin, have moved ahead of Uzbekistan into third spot, with their win over Qatar eliminating the 2022 World Cup hosts.
The top two in each group qualify automatically for the finals, while teams finishing in third place enter a series of playoffs, with China's win ensuring Italian Marcello Lippi's side have retained their slim hope of qualification.
"I've been telling my players that, as long as there was a theoretical chance of qualifying that we should try our best," said Lippi, whose team moved up to fifth following a debatable penalty scored by Gao Lin in the 84th minute.
"It was already a miracle that we made it to the final 12 and we don't have any reason to give up. Today, we are happy. We won and we made our fans happy."
Syria travel to Tehran on Tuesday to face an Iran side yet to concede a goal in qualifying, while Uzbekistan host South Korea in Tashkent and China travel to Doha to take on bottom side Qatar in the final round of group matches.
(Reporting by Michael Church, Editing by Ken Ferris)
