Japan moved into an automatic qualification spot in Group B of Asia's World Cup qualifying section with a 2-0 victory in the United Arab Emirates.

A 2-1 home defeat to UAE at the beginning of the third round of qualifying put Japan on the back foot in a heavyweight group that also includes Saudi Arabia and Australia.

However, goals from Yuya Kubo, his first at international level, and Yasuyuki Konno helped Vahid Halilhodzic's side vault above the Socceroos, who drew away to Iraq, and into second place, behind the Saudis on goal difference.

Defeat keeps UAE fourth in the pool and a crunch clash at home to Australia on Wednesday (AEDT) now looks set to be pivotal to both sides' hopes of making it to Russia next year.

UAE had won each of its last three home games prior to the match, but Japan struck early to wrest control of the contest, taking the lead in the 13th minute as Hiroki Sakai's pass down the channel put Kubo behind the defence and he smashed home first time.

Ali Mabkhout should have levelled the scores soon after, but the 26-goal UAE Pro League top scorer could not beat a sprawling Eiji Kawashima one-on-one.

Home star Omar Abdulrahman was shackled throughout and his frustrations spilled over when he stretched for a chipped pass, but caught Kawashima with his studs and was booked.

There were more missed chances for the host after half-time, Ismail Al Hammadi produced an air shot with the goal gaping from Abdelaziz Sanqour's cross, with the latter then seeing a close-range effort charged down before Japan marched up the other end and secured breathing space.

Kubo turned provider as his cross from the right found Konno stealing in at the back post and the veteran midfielder prodded in just his third goal in 88 international appearances.

Japan hosts bottom team Thailand on Tuesday, a game in which it will be expected to cement second place at least.