The 12 winners from the second round were divided into 3 groups of 4. The winner of each group advanced to the Olympic Games while each runner-up advanced to the play-off round. The draw was held on July 7, 2011 in Kuala Lumpur, Malaysia.
Matches were played on 21 September 2011, 23 and 27 November 2011, 5 and 22 February 2012 and 14 March 2012.
The three runners-up from the third round groups played each other at a neutral venue on 25, 27 and 29 March 2012. Malaysia had originally been chosen but renovations to the proposed stadium as well as the unavailability of other venues due to the scheduling of domestic fixtures meant that a new destination for the three-team playoffs was required. Vietnam was later chosen by the AFC Competitions Committee as the neutral venue, with games played at Hanoi's My Dinh Stadium
Oman was the winner of this group advanced to play Senegal in a play-off for a spot at the Olympic Games.