Mehdi Mehdikhani fired into the top corner to gave Team Melli a lead.
Mohammad Hossein Derakhshani, easily turned the ball in at the back post, minutes later.
After the interval, the pattern of the game remained the same with Iran dominating play but unlike the first half, found the Malaysian defense tougher to breach.
Iran's persistent pressure was rewarded late in the half with Hossein Tayebi pouncing on a rebound in the 33rd minute before Ali Khalilvand looped a header over Malaysian custodian Syaifuddin Syukri to seal qualification for the 13-time champion.
Iran finished top of the group with three wins with Malaysia coming second on six points.
The other match saw the United Arab Emirates conclude its campaign in style with an 8-2 win against Bangladesh.