The two teams met at the Al Rayyan Stadium on Wednesday in their last group stage match.
The UAE team had to beat Iran, which had already qualified, to keep their hopes of advancing to the knockout stage alive.
The UAE’s Ismail Matar created a good chance with just one minute remaining in the first half but his shot fell wide of the far post.
in the second half, Mohammad Gholami’s header hit the bar and Arash Afshin found the back of the net in the 70th minute to give Iran a 1-0 lead.
Iran’s Arash Afshin was sent off five minutes later after collecting his second yellow card. Khalid Sebil of the UAE was also forced to leave the pitch after receiving his second yellow card.
Mohammad Nouri poured cold water on the UAE’s hopes by scoring Iran’s second goal in the 83rd minute.
The UAE’s Ali Abbas scored an own goal in extra time to give Iran its third goal.
Iran’s Andranik Teymourian was named the player of the match.
Iran is scheduled to play South Korea at the Qatar SC Stadium on Saturday.
In other Group D action, the Iraqi national football team qualified for the next round with a 1-0 victory over North Korea and will play Australia in the quarterfinals.
The Iraqis sent the Socceroos packing at the previous edition of the AFC Asian Cup, which was held in Malaysia in 2007.