Asano steered home a left-foot volley four minutes before half-time and Ideguchi sealed the victory with a stunning long-range strike after 82 minutes as Japan became the fourth team to reach next year's finals in Russia.
The result dealt a major blow to Australia's chances of being one of the two automatic qualifiers from Group B after their first defeat in the final round of Asian qualifiers.
The Asian Cup holders get a second bite at the cherry at home to Thailand on Tuesday when they need to better Saudi Arabia's result against Japan in Jeddah on the same night.
Yuto Nagatomo whipped in a cross from the left and Asano ghosted in to beat goalkeeper Mat Ryan from close range.
Australia threw on veteran Tim Cahill after 70 minutes to try and inject some spark and his industry almost brought an equaliser for fellow substitute Tomi Juric.
But Japan effectively ended Aussie hopes when Ideguchi cut inside to slam a right-foot shot past Ryan from distance for his first international goal.
"That's my job -- to try and pinch goals and I'm always ready to give everything for Japan."
Japan had never beaten Australia in a World Cup qualifier in seven previous attempts but the Socceroos -- bidding to reach their fourth straight finals and fifth overall -- rarely threatened in a disjointed performance.
"This is for the wonderful fans and for the people of Japan," cried Japan's under-fire coach Vahid Halilhodzic, whose team have an unassailable 20 points from nine games in Group B.
Ideguchi, meanwhile, appeared lost for words after a wonder strike that looks like sparing Halilhodzic the sack -- at least for now.
"Luckily it hit the target," he said sheepishly. "I'm just glad it helped us get the win and hopefully I can keep working to get myself picked for the World Cup."
Brazil and Japan's Asian rivals Iran have already qualified for next year's World Cup, alongside tournament hosts Russia.
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