The draw for the group stage was held on 6 December 2012, 15:00, at the AFCHouse in Kuala Lumpur, Malaysia. The 32 teams were drawn into eight groups of four. Teams from the same association could not be drawn into the same group. The following 32 teams were entered into the group stage draw, which included the 31 automatic qualifiers and the qualifying play-off winner, whose identity was not known at the time of the draw: ;West Asia Zone
Al-Muharraq withdrew after the draw was held. As a result, Regar-TadAZ, which were initially to enter the qualifying play-off, instead directly entered the group stage, and only two teams participated in the qualifying play-off.
Format
In the group stage, each group was played on a home-and-away round-robin basis. The winners and runners-up of each group advanced to the round of 16.
Tiebreakers
The teams are ranked according to points. If tied on points, tiebreakers are applied in the following order:
Greater number of points obtained in the group matches between the teams concerned
Goal difference resulting from the group matches between the teams concerned
Greater number of goals scored in the group matches between the teams concerned
Goal difference in all the group matches
Greater number of goals scored in all the group matches
Penalty shoot-out if only two teams are involved and they are both on the field of play
Fewer score calculated according to the number of yellow and red cards received in the group matches
Drawing of lots
Groups
The matchdays were 5–6 March, 12–13 March, 2–3 April, 9–10 April, 23–24 April, and 30 April–1 May 2013.
Group A
;Tiebreakers
Al-Riffa are ranked ahead of Safa on head-to-head record.
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Group B
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Group C
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Group D
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Group E
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Group F
;Tiebreakers
New Radiant and Yangon United are tied on head-to-head record, and so are ranked by overall goal difference.
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Group G
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Group H
;Tiebreakers
Selangor are ranked ahead of Sài Gòn Xuân Thành on head-to-head record.
