Anvar Gafurov and Bakhodir Nasimov scored either side of half-time for the Uzbeks before Baddrol Bakhtiar pulled a goal back for Malaysia with 20 minutes remaining.
But captain Timur Kapadze restored the advantage three minutes later as Uzbekistan recorded a third consecutive win to extinguish any hope an under-strength Malaysia had of reaching the finals in Qatar.
Uzbekistan join the host nation, AFC Challenge Cup winners India and the top three at the 2007 finals - Korea Republic, Iraq and Saudi Arabia - in the showpiece event.
"We have qualified for the Asian Cup but now we will have to make sure that we complete the fixtures on a winning note," said coach Mirdjalal Kasimov. "But it was not a performance which was deserving of praise."
Syria's 0-0 draw at home to Vietnam in Aleppo put them on the verge of making the finals. They now have ten points in Group D and only a major upset will prevent them progressing.
China are favourites to join them, and they play Lebanon in Beijing on Sunday.
Asian powerhouse Japan remain firmly on course after they comfortably overcame a spirited Hong Kong side, a trademark left-footed free-kick from Espanyol's Shunsuke Nakamura the highlight at a half-full Hong Kong Stadium.
"We knew all about Singapore's set pieces. We spoke about it and worked on it in training. On the goal, our marking was wrong," said Thai boss Robson after the defeat. "That game should have been 0-0."
Singapore's win win saw them leapfrog their south-east Asian neighbours to second in Group E, a point behind Iran who have played a game fewer.
Kuwait, meanwhile, ground out a 1-1 draw with Indonesia in Jakarta to put them level on seven points with Australia in Group B. Oman have four points and Indonesia three.
Later on Wednesday, Bahrain will look to bounce back from the disappointment of missing out on the 2010 FIFA World Cup™ when they take on Yemen at home.
Milan Macala's side were devastated after their 1-0 loss to New Zealand in the second leg of the AFC-OFC play-off on Saturday which deprived them of a place in South Africa 2010.
Bahrain though are well-placed to make the Asian Cup, with maximum points from two games so far.