Former champions Jeonbuk drew 2-2 at home to Jiangsu FC of China which kept them top of Group E, level on 10 points with Tokyo who they lead due to a superior head-to-head record.
The top two qualified for the last 16 in the continent's premier club competition with Jiangsu finishing a point behind in third and Becamex bottom of the standings on four points.
Tokyo, who had to win to progress, dominated possession and took the lead in the 21st minute when Maeda headed home from close range before scoring his second with a sublime strike 10 minutes after the break.
Le Cong Vinh netted a penalty 13 minutes later to make it 2-1 after Cameroonian Christian Amougou was brought down and he almost equalised late on when his curling effort hit the bar.
The Japanese side were almost left to rue their wasted opportunities earlier in the match but held on to bag the crucial three points and reach the knockout phase.
Leonardo's penalty gave hosts Jeonbuk the lead in the 19th minute at the Jeonju World Cup Stadium but the Chinese Super League side equalised through Brazilian Alex Teixeira.
His compatriot Jo scored from the spot to give the visitors a 2-1 lead nine minutes after the break.
Lim Jong-eun headed an equaliser in the 68th minute much to the relief of the 40,000 plus crowd as the 2006 champions clinched a fourth straight appearance in the knockout stages.
FC Seoul, already into the last 16, lost 2-1 at Japanese champions Sanfrecce Hiroshima but won Group F ahead China's Shandong Luneng, who drew 0-0 at Thailand's Buriram United.
Takuma Asano and Yusuke Minagawa scored before halftime at the Hiroshima Athletic Stadium to give the hosts a 2-0 lead before Seoul's Brazilian Carlos Adriano scored his 10th goal in six matches in the competition with an 88th minute penalty.
(Reporting by Sudipto Ganguly in Mumbai; Editing by Ken Ferris)
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