Indonesia and North Korea also confirmed their progression to the next round with the Chinese qualifying as runners-up in Group C behind the South Koreans after Thailand could only register a 3-1 victory over Singapore.
Needing to win by three clear goals, or to score at least four with a two-goal victory margin, to climb above the Chinese in the standings, Masatada Ishii's side fell agonisingly short of a spot in the draw for the next round on June 27.
Suphanat Mueanta put Thailand in front eight minutes before the break but Thailand-based forward Ikhsan Fandi levelled 12 minutes after the restart for the Singaporeans.
A frantic Thailand pushed forward as time ticked down with Poramet Arjvirai and Jaroensak Wonggorn scoring in the last 11 minutes to take their side closer to their target, but ultimately the War Elephants fell short.
The Chinese had earlier lost in Seoul World Cup Stadium when Paris Saint-Germain winger Lee Kang-in scored from close range in the 61st minute to leave Branko Ivankovic and his players sweating on the outcome of the game in Bangkok.
Indonesia, meanwhile, confirmed their progression to the third round for the first time with a comfortable 2-0 win in Group F over the Philippines at a buoyant Gelora Bung Karno Stadium in Jakarta.
Netherlands-born midfielder Thom Haye put the home side in front 32 minutes into the game when he bent a perfectly judged right foot shot into the top corner of Kevin Mendoza's goal.
The victory was secured through a glanced header by Rizky Ridho in the 56th minute that gave the unprotected Mendoza little chance as Indonesia confirmed a second-place finish behind Iraq.
Japan cruised to a 5-0 win over Syria in Hiroshima that fatally damaged the hopes of Hector Cuper's side, who were overtaken in second place in Group B by North Korea as a result of their 4-1 win over Myanmar in Vientiane.
Australia, who had already confirmed their place in the next round, notched up a 5-0 win over Palestine in Perth to finish Group I with a perfect record.
Later on Tuesday, Kyrgyzstan take on Oman needing to avoid a heavy defeat to advance from Group D alongside the Gulf nation after Malaysia recorded a 3-1 win over Taiwan.
