Needing a win to claim second spot in Group Four, and for Saudi Arabia to lose in Australia, Oman took just nine minutes to break the deadlock through Hussain Al Hadri.
Thailand battled hard for an equaliser but the dismissal of Teeratep Winothai five minutes from time effectively ended their challenge, with Abdul Aziz Mubarak making it 2-0 in the dying seconds.
Saudi Arabia twice threw away the lead in a 4-2 loss against group winners Australia, leaving them third in the pool.
The Saudis were in front after 19 minutes through Saleem Al Dawsari, and although Alex Brosque levelled matters in the 43rd minute, the visitors restored their lead two minutes later thanks to Nasser Al Shamrani.
But three goals in three second-half minutes from Harry Kewell (73), Brosque (75) and Brett Emerton (76) ended Saudi Arabia's hopes of reaching the next stage of the qualifying competition.
In Group Three, winners Uzbekistan preserved their unbeaten record with a 1-0 victory over nearest rivals Japan.
Alexander Shadrin scored the only goal nine minutes after the interval, although both teams had already sealed places in the next round.
The pool's other match between Tajikistan and North Korea ended in a 1-1 draw.
A 54th-minute penalty from Jang Song-Hyok gave the visitors the advantage, but Tajikistan were back on level terms eight minutes later through Akhtam Khamroqulov.
Already-qualified Jordan ended their Group One campaign with a 3-1 defeat in China.
Hao Junmin scored twice for the Chinese, after 43 and 69 minutes. Abdallah Salim replied for the visitors five minutes from time but Yu Dabao had the final say moments later with China's third.
Jordan's defeat allowed Iraq to claim top spot in the group with a 7-1 thrashing of winless Singapore.
Younis Mahmoud grabbed a hat-trick for the home side with Karrar Jasim, Hawar Mulla Mohammed, Nashat Akram and Mustafa Kareem also on the scoresheet.
Singapore's only reply came from the boot of Mohammad Abdul.
South Korea secured their place in the next round and finished top of Group Two with a 2-0 victory over Kuwait.
Lee Dong-Gook fired the opener after 65 minutes with Lee Keun-Ho adding another six minutes later, ending Kuwait's challenge in the competition.
Lebanon had to settle for second spot in the pool after falling to a 4-2 loss against the United Arab Emirates.
Basheer Saeed's 20th-minute strike for UAE was cancelled out by Mahmoud El Ali three minutes later.
Saeed scored again after 38 minutes but the home side were once more pegged back by an equaliser from Hassan Maatouk at the end of the first half.
However, a 70th-minute effort from Ismaeil Matar restored UAE's lead before Saeed completed his hat-trick 11 minutes from time to end the contest.
In Group Five, Iran held on to first place with a 2-2 draw against Qatar in their top-of-the-table match.
Ashkan Dejagah twice gave Iran the lead, but an Ibrahim Khalfan penalty and a late goal from Kasola Mohammed ensured the points were shared.
Third-placed Bahrain brought the curtain down on their campaign with a stunning 10-0 rout of hapless Indonesia.
Mohamed Tayeb and Sayed Dhiya both hit hat-tricks for the winners, with Ismael Abdullatif and Mahmood Abdulrahman adding braces.
Wednesday's 2014 AFC World Cup Qualifying Results
China 3-1 Jordan
Iraq 7-1 Singapore
Korea Republic 2-0 Kuwait
United Arab Emirates 4-2 Lebanon
Tajikistan 1-1 Korea DPR
Japan 0-1 Uzbekistan
Australia 4-2 Saudi Arabia
Oman 2-0 Thailand
Bahrain 10-0 Indonesia
Iran 2-2 Qatar