A positive performance in the early part of the first half provided a valuable victory over the hosts, who still are without a point in the third round of qualifying
The defeat extended Indonesia's poor performance in the third round of qualifiers with their fifth consecutive defeat, while Team Melli all but secured their passage into the next round.
One minute into the first half, Iran already had an opportunity through skipper Javad Nekounam who shot wide, but it was a warning sign for the hosts, who had already been eliminated from contention to qualify for the next round.
A minute later, Indonesia broke on a counterattack but Uruguay-born Cristian Gonzales' shot was weak and was easily saved by Iran keeper Mehdi Rahmati.
Iran's early barrage of attacks finally proved fruitful on seven minutes after a slip by Indonesia left-back Mahyadi Panggabean allowed Milad Meydavoudi in to make it 1-0.
In the opening quarter of an hour in the game, Carlos Queiroz's team dominated, both in terms of ball possession and opportunities. The second goal came when Mohammad Ghazi broke in behind the Indonesia defence, before playing a central ball for Mojtaba Jabbari to tap in.
Not long after the second goal, Gholamreza Rezaei made it 3-0 for Iran from a sharp angle after another mistake, this time from keeper Kartiko.
Merah Putih created a few opportunities, with captain Bambang Pamungkas offering his side hope when he netted one minute prior the end of first half, thanks to Samsul Arif's cross.
In the second half, Iran played more carefully and Indonesia pressed on with several opportunities created with Rahmati's goal threatened by the trio of Gonzales, Bambang and Firman Utina.
However, the hosts couldn't find a way through and Nekounam sealed the win with a penalty in the 72nd minute, after Mohammad Reza Khalatbari's penetrating run led to a foul by Benny Wahyudi inside the area.
In the dying minutes of the game, Iran missed a chance for another when Reza Khalatbari's shot wide of Kartiko's goal, and the clash ended 4-1.
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