Abdulrahman converted a free kick five minutes into added time to leave the woeful Uzbeks, the best-performing team in earlier rounds, rooted to the bottom of the Group One table.
Bahrain moved third, four points behind Japan and six adrift of leaders Australia, who played out a goalless draw in Yokohama.
"It's a very good result for us," Bahrain's Czech coach Milan Macala told reporters.
"We still have some away matches and I hope that we will battle for second spot in this group."
Anzur Ismailov looked to have put the Uzbeks ahead in the first half when he fired into the net after a corner from Asian player of the year Server Djeparov, which was adjudged to have gone out of play.
They piled on the pressure in the second half and came close when Farhod Tadjiyev fired wide of the post from the edge of the box.
The hosts almost clinched the winner five minutes from time when Anvarjon Soliev shot wide when following up a rare botched effort by prolific striker Maksim Shatskikh.
The defeat severely dented Uzbekistan's hopes of reaching the finals for the first time having come within two games of the 2006 tournament.
The top two teams in each group qualify for South Africa 2010 while the two third-placed sides will playoff for a chance to take on Oceania winners New Zealand for one more berth.
"We were unlucky to miss a lot of chances," said Uzbekistan coach Mirdjalal Kasimov.
"Our players did not follow instructions...we lost but we will fight for every point in the remaining matches."
