Southeast Asian champions Malaysia, who will meet arch rivals Singapore in the next round, conceded three penalties in a 3-2 defeat in Taipei on Sunday having won the first leg 2-1.
First-half goals from Mohamed Aidil Abd Radzak and Safiq Rahim had given Malaysia a 2-1 lead and they appeared to be comfortably heading into the next round before spot-kicks by Chen Po-liang and Xavier Chen put the hosts ahead to set up a nail-biting final 15 minutes.
Malaysia goalkeeper Mohd Sharbinee Allawee Ramli had also saved a 61st-minute penalty from Chen which proved vital.
Vietnam striker Le Cong Vinh followed up his first leg hat-trick with five goals on Sunday as Vietnam hammered hapless Macau 7-1 for a 13-1 aggregate victory.
Cong Vinh scored three goals in the first half and added two more in the second as Vietnam, who will meet 2022 hosts Qatar in the second round, piled on the misery on Macau after a first-leg drubbing.
Laos booked a second-round meeting with China after scoring twice in extra time to defeat Cambodia 6-2 for an 8-6 aggregate victory.
The teams had been level on aggregate at the end of normal time after Cambodia had won the first leg 4-2 but goals from Visay Phaphovanin and Sysomvang Kanlaya put Laos through.
Palestine's 1-1 draw with Afghanistan on Sunday was enough to send them through to a second-round tie against Thailand after a 2-0 first-leg victory.
Myanmar defeated Mongolia 2-0 to overturn a 1-0 first-leg deficit while Nepal set up a second round encounter with Jordan with an emphatic 5-0 win against Timor-Leste after beating them 2-1 in the first leg.
Eight first-round winners join 22 higher ranked teams in the second round of the Asian qualifiers to be played on July 23 and 28.
Australia, Japan, both the Koreas and Bahrain - the continent's top five teams in South Africa 2010 qualifying - will automatically enter the third round.
Four Asian teams will qualify directly for the World Cup in Brazil while one will have the chance to make the finals via a two-leg play-off.
