Germany-based striker Yuki Otsu scored with four minutes remaining to ensure Japan stole three points.
The top of the table clash in Group C appeared to be heading for a draw after Syria's Omar Al Suma struck with 15 minutes remaining at the National Stadium to cancel out Mizuki Hamada's first half opener.
But Borussia Monchengladbach's Otsu, who scored in Japan's 2-0 win in Bahrain last week, netted to hand Japan a three point lead over Syria at the halfway stage of the campaign, with only the three group winners guaranteed to represent Asia in London next year.
Bahrain, meanwhile, boosted their chances of claiming second place in Group C, which would be enough to earn a place in a play-off for the right to meet an African representative for ticket to London, after scoring three goals in the final 10 minutes to beat Malaysia 3-2 in Kuala Lumpur.
With both teams beginning the final round with back-to-back defeats by Syria and Japan, Malaysia looked on course to build on their SEA Games gold medal triumph as goals in each half from Muhammad Nazmi and Amer Saidin had put the home side into a seemingly commanding position at Bukit Jalil Stadium.
But despite playing the final 20 minutes with 10-men after Fahad Showaiter was sent-off, Bahrain reduced the deficit with 10 minutes remaining through Saad Al Amer's spectacular bicycle-kick.
And after Isa Al Ahmed's equally eye-catching free-kick pulled the visitors level four minutes later, the substitute striker struck again with two minutes remaining to leave Bahrain three points adrift of Syria with three games remaining in February and March next year.
In Group A, Korea Republic maintained their unbeaten record as Cho Young-cheol's 33th minute penalty was enough to edge out Saudi Arabia 1-0 at Seoul World Cup Stadium.
Korea, who drew 1-1 with Qatar in Doha last Wednesday, moved three points clear of Oman at the top of the table after unbeaten Qatar snatched a point in Muscat on Sunday.
Oman appeared to be heading for a second consecutive win in Group A following last week's 2-0 home win over Saudi Arabia as Abdul Aziz Al Maqbali struck after 11 minutes at Al Seeb Sports Stadium.
But with just two minutes remaining, Fahad Khalfan netted for the visitors as Qatar recorded a third consecutive draw to sit just a point further off the pace at the halfway mark.
Finally in Group B, Uzbekistan and Australia also remained unbeaten after sharing a goalless draw in Sydney, while Iraq recorded a first win of the campaign after beating the United Arab Emirates 2-0 in Al Ain.
Abdulraheem Karrar and Sabah Al-Hlaichi scored in each half at Sheikh Khalifa International Stadium as Iraq moved up to second place, one point behind leaders Uzbekistan, with Australia a further point adrift after being forced to settle for a third consecutive goalless draw of the campaign.