Majed Mohamed (37th minute), Yussef Ahmed (39, 64), Ali Hassan (41), Adel Lami (43), Talal Al Beloushi (69) and Waleed Jassim (73) were the scorers for the winners.
Pakistan lost all the home and away matches of the round against Qatar, Bahrain and Kuwait.
Iran, Oman, UAE, Kuwait, India and Pakistan were ousted from the qualifiers as the final round of the AFC qualifiers for the 2008 Beijing Olympics ended on an exciting note.
Australia, Uzbekistan, Vietnam, Syria, Bahrain and Qatar have confirmed their spots. The six teams join Japan, Lebanon, Saudi Arabia, DPR Korea, Iraq and South Korea.
In Manama, Jesin John’s 90th minute strike settled the encounter against Kuwait in favour of Bahrain 2-1. Fati Baba Tonde scored the first Bahrain goal in the 23rd minute but Kuwait neutralised it in the 23rd minute through Abdullah Masheleh’s penalty.
Japan ended their campaign with a 3-1 win against Malaysia in Tokyo for a perfect record of six straight wins in Group B. Syrians beat Hong Kong 4-1 in Damascus. Vietnam made sure of their place in the final with a 2-1 win over Indonesia, thanks to a brace by Nguyen Vu Phong in Group C.
In Group D, Nick Ward hit a brace as Australia crushed hosts Jordan 4-0 to qualify for the next round in Amman. The Saudis, meanwhile, ended Iran's hopes of advancing by beating them 3-2 at the Azadi Stadium in Tehran.
In Group E, Iraq completed their campaign on a victorious note with a 1-0 win over fellow group qualifiers DPR Korea and took the top position in the pool. In the meantime, Thailand beat India 2-0 in the other group game.
In Group F, Shavkat Salomov netted a brace and guided Uzbekistan to a 3-0 win over Yemen. The UAE lost to South Korea 1-3 in the other group game.