The qualifying round for the lower ranked teams in Southeast Asia was held in Bacolod, Philippines from 12 to 20 November 2006.

If the total aggregate score of both teams after both matches remained the same, extra time would have been played, followed by a penalty shootout if necessary.

In the first leg of the final, a controversial penalty was awarded to Singapore at the 83rd minute of the match, and the Thailand team walked off the pitch as a protest to the referee's decision.

In the second leg of the final, Singapore had a goal controversially chalked off for being offside, but finally drew 1-1 to fellow Thailand, with Khairul Amri scoring the decisive goal in the closing stages of the match, giving Singapore their 2nd title in succession, winning with an aggregate score of 3-2 and successfully defending the title.

It could have been worse for Thailand had the match officials seen Thai midfielder Datsakorn Thonglao headbutt Singapore's Khairul Amri to vent his anger after the equaliser.