Dominating the game throughout, Takashi Sekizuka's side opened the scoring in the tenth minute after midfielder Keigo Higashi latched onto a defence-splitting pass to slot the ball beyond the Malaysian goalkeeper.
The home side frayed their supporters' nerves, spurning several good chances and finding Malaysian keeper Khairul Fahmi Che Mat in top form. However, a 76th-minute strike from substitute Ryohei Yamazaki secured the three points.
"We had the first goal early on in the game. Our plan was to defend the lead and go for additional goals," said Japan coach Sekizuka adding his side would need to be less profligate against fellow Group C teams Bahrain and Syria.
Korea Republic also scored two without reply to beat Oman in Changwon, courtesy of a glorious 23rd-minute free-kick from Yoon Bitgaram and a nicely taken second in the 74th minute by Cerezo Osaka midfielder Kim Bo Kyung.
Yoon, who won the foul just outside the box, got up to take the free-kick and angled the ball into the top right of the net. He turned provider in the second-half feeding Kim to seal the win.
The Koreans are paired with Oman, Qatar and Saudi Arabia in Group A and their next game will pit them against Qatar on 23 November.
Going into the match as favourites to win their group, the Australians were outplayed by the visitors for large periods of the match. UAE striker Ahmed Khalil menaced the Aussie goal throughout the first half, blasting just wide from 25 yards out after the half-hour mark with goalkeeper Andrew Redmayne beaten.
Khalil nearly broke the deadlock three minutes later after finding the net only to have the goal ruled offside. Australia had two golden chances of their own to turn the tide in the second half, both courtesy of influential Brisbane Roar midfielder Mitch Nichols.
Nichols failed to latch on to an inviting 59th-minute cross and steered a diving header into the hands of UAE goalkeeper Adel Mohamed ten minutes later. Australia, who routed Yemen 7-0 over two legs to reach the group stages, will be determined to raise their game against their other Group B opponents Iraq and Uzbekistan.
The 12 teams jostling for a berth at the London Games are divided into three groups of four and play each other home and away. The winners qualify for the Olympics automatically, while runners-up in each group play a three-way round-robin.
The winner of that contest enters a play-off with a side from the African confederation to advance to next summer's showpiece event. The group stage wraps up in March next year.