In Manama, midfielder Alaa Hubail was the hero for the hosts, scoring in the 77th minute to move Bahrain to the top of Group 2, unbeaten after two matches.
Earlier in the day, China's Shao Jiayi had a last-gasp penalty saved and Korea Republic were frustrated by the Korea DPR's stubborn defence as some of Asia's top teams failed to find the net.
Group 1 favourites Australia remain provisionally top the section with Asian champions Iraq playing Qatar later in the second round of matches Wednesday.
Uzbekistan went top of Group Four after an impressive 3-0 win over Saudi Arabia in Tashkent. The home side took the lead on the stroke of half-time through Timur Kapadze's header before Maksim Shatskikh doubled the lead midway through the second half and a Server Djeparov penalty shortly afterwards sealed victory.
Iran take their bid for a fourth FIFA World Cup appearance to Kuwait in Group 5, which also saw Gulf champions United Arab Emirates snag a 1-1 away draw with Syria.
Chinese midfielder Shao was distraught after scuffing his penalty in the dying minutes against Australia in front of 32,500 baying home fans in Kunming.
Goalkeeper Mark Schwarzer dived low to his left in the 88th minute to block Shao's shot as Australia escaped the tricky tie with a point.
"I must apologise to the team and the fans for that penalty
kick," Shao said. "Because of me we did not win the game.
We should have won the game but we didn't because I missed the
penalty kick. I really feel bad about this."
Australia should have been firm favourites but they had only two days to acclimatise to Kunming's 1,900-metre (6,233-foot) altitude and a long injury list including Everton's Tim Cahill and Celtic striker Scott McDonald.
Given the difficulties, coach Pim Verbeek was happy with the result, which maintained his unbeaten record and kept Australia on course for South Africa 2010.
"The boys played very hard to get this result. Of course we came here to win because everyone likes to win games. But I have to admit, I can live with this result," said the Dutchman.
Meanwhile, Korea Republic were kept out by stout North Korean defending as their much-anticipated showdown also ended in a goalless stalemate.
The South, despite fielding top stars such as Manchester United's Park Ji-Sung, failed to convert a series of chances in the Cold War clash, which was moved from Pyongyang to Shanghai in a row over flags and anthems.
"We should have won this match," said Park, who joined up with the squad on Tuesday. "We couldn't finish around the net."
Fulham's Seol Ki-Hyeon, Cho Won-Hee and Park Chu-Young all went close for South Korea, while the North's Jong Tae-Se had a close-range shot deflected wide.
The top two teams from each of five groups will reach the fourth and final Asian qualifying round for the 2010 tournament.