Iran was the dominant side in the first half but failed to score, thanks to Indonesia's determined defense and good saves by goalkeeper Marcos. Indonesia relied on sporadic counter-attacks.
Osasuna midfielder Nekounam opened the scoring in the 54th minute with a header and headed in again in the 73rd.
Substitute Andranik Teimourian scored Iran's third goal with a volley from outside the box to give the favorites a deserved victory in front of a crowd of about 70,000 in Tehran's 100,000-capacity Azadi Stadium.
Bahrain and Qatar are the other two teams in Group E. Iran will take on Qatar in Doha on Sept. 6 while Indonesia will host Bahrain in the same group.