Australia were just four minutes from a shocking home draw with Thailand before Alex Brosque's late strike, while Japan had to wait until the 94th minute to overcome fierce rivals Korea DPR in rain-lashed Saitama.
China also had to fight back from a goal down before beating Singapore 2-1 at home in former Real Madrid and Spain coach Jose Antonio Camacho's first game in charge.
However, Korea Republic hit six past stunned Lebanon in Goyang to take a decisive first step on the road to Brazil 2014 as Asia's top-ranked sides entered the lengthy qualifying process, which will end next year.
Teerasil Dangda gave the visitors a shock lead on 15 minutes and Australia were not back on terms until Josh Kennedy's 58th minute strike, before Brosque's last-gasp decider relieved Brisbane's Suncorp Stadium crowd.
"It feels like a loss," Schwarzer said. "It was one of our worst performances for a long time and there are no excuses, we weren't good enough at times, but at least we won which is the positive."
The Blue Samurai had dominated play despite missing midfield duo Keisuke Honda and Kengo Nakamura through injury, and coach Alberto Zaccheroni said the result was a just reward for their patient play.
"I think the Koreans played their 100 per cent. We had to be patient, patient, patient, but we were threatening them repeatedly and finally Maya scored a goal," said Zaccheroni. "We were on the offensive for most of the time and I just waited for the goal for a long time."
Park treble lifts Koreans
In Goyang, Park Chu-Young celebrated this week's move to Arsenal with a hat-trick as Korea Republic ran riot against the Lebanese.
Park, who was signed from AS Monaco, set the South Koreans on their way with two goals in the first half before completing his treble on 67 minutes. Sunderland forward Ji Dong-won scored twice and Kim Jung-woo once.
Aleksandar Duric capitalised on a break to put the visitors in front on 33 minutes, but the arrival of Zheng from the bench in the 67th minute swung the game in favour of the Chinese.
Zheng slotted a penalty - China's second of the night, after Qu Bo's effort was saved ten minutes earlier with virtually his first touch, and he was also involved in the move that led to Yu Hai's winner with 12 minutes remaining.
Uzbekistan edge Tajikistan
Meanwhile, the ever-reliable Maksim Shatskikh's 72nd-minute goal gave Uzbekistan a 1-0 away win against Tajikistan, who are only in the draw after Syria were disqualified for fielding an ineligible player.
The winners and runners-up of the third round's five groups will be drawn into two pools for the round-robin fourth stage, with the eventual top two in each section earning a ticket to Brazil.
The two third-placed teams will then face each other for the right to contest an intercontinental play-off.