Milad Midavoodi broke the deadlock with just seven minutes at the Gelora Bung Karno played before his Esteghlal team-mate Mojtaba Jabari doubled Iran's lead 12 minutes later.
The red side of Tehran were soon represented on the scoresheet with Persepolis (Piroozi) forward Gholamreza Rezaei hitting the target in 24th minute to extend Iran's advantage, which was reduced two minutes from the interval when Indonesia's star striker Bambang Pamungkas finally gave the home side something to cheer about.
Iran restored their three-goal cushion midway through the second-half when Javad Nekounam successfully converted a 72nd minute penalty with the Iran skipper's spot-kick sealing the victory that took Team Melli's points tally to 12 while defeat left Indonesia still without a point to their name.