Goals from Takuma Asano and Yosuke Ideguchi ensured a sixth successive place in the finals for Asia's second-ranked nation.
Japan beat Australia to win UAE's group and qualify for 2018 World Cup
Japan are the first nation from the UAE's group to qualify for the 2018 World Cup after a 2-0 victory over Australia in Saitama on Thursday.
Takuma Asano and Yosuke Ideguchi were on target for the hosts, who have booked their place at a sixth successive World Cup.
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.
For the UAE to stand a chance of automatic qualification, they need to beat Iraq on Tuesday, hope Australia lose to Thailand and Saudi Arabia lose to Japan by enough of a margin to ensure an eight-goal swing on both sides.
Even if Australia collect a least a point against Thailand, the UAE can still clinch third spot, and thus passage into the playoffs, if the Saudis lose to Japan with the eight-goal swing still needed.
But any permutations will not apply to Japan, who put their opening group defeat to the UAE behind them to win six and draw one of their matches.
"I was looking for a chance and Yuto put in a great ball," said Asano of his opening 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 visitors - 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," said Japan manager 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 booked his nation's place in Russia.
"Luckily it hit the target," he said. "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.