On a frantic day of action across Asia, with 14 matches played, Iraq, Oman, China, Vietnam and Lebanon also made it through after finishing among the five best second-placed teams.
Syria, Japan, South Korea and Australia had already clinched their spots in the deciding round, from which four countries will advance to next year's tournament in Qatar.
Qatar, who topped Group E, will not play in the final phase as they qualify automatically as hosts.
On Tuesday, Iran pipped Iraq 1-0 in Bahrain to top Group C while the UAE edged Vietnam 3-2 in their final Group G match in Dubai.
To qualify, both Iran and the UAE needed to topple the teams that went into the final round of matches leading their groups. They did it in contrasting styles.
Sardar Azmoun fired Iran ahead in the 35th minute at the Sheikh Ali bin Mohamed al-Khalifa Stadium in Muharraq.
The Zenit Saint Petersburg striker, who has played a pivotal role for his team since the qualifiers resumed, tapped in from close range after captain Ehsan Hajsafi made his way up the left flank and sent in a cross.
Both teams fluffed chances later but Iran hung on to their lead to take their tally to 18 points from eight matches, while Iraq finished on 17.
Meanwhile in Dubai, Vietnam wasted their two-point advantage at the top as they were beaten by the Emiratis with Ali Salmeen and Ali Mabkhout finding the net in the first half.
Mahmoud Khamis made it 3-0 five minutes after the break, and while Vietnam pulled two late goals back through Nguyen Tien Linh and Tran Minh Vuong it wasn't enough to keep top spot.
China's also needed to winn their last match and they did that comfortably with a 3-1 victory over Syria.
Zhang Xizhe, Wu Lei and Zhang Yuning scored for China in Sharjah. Syria's goal was scored by Aias Aosman.
Elsewhere, Salman al-Faraj scored a brace as Saudi Arabia thrashed Uzbekistan 3-0 to clinch top spot in Group D.
Ali al-Hassan added a third in the second half as the Saudis took their tally to 20 points from eight matches.
Already-qualified Australia edged Jordan 1-0 to record their eighth consecutive win in the second phase. Harry Souttar scored the only goal.
Earlier striker Ado Onaiwu bagged a six-minute first-half hat-trick as Japan confirmed their dominance in Group F with a crushing 5-1 win over the Kyrgyz Republic in Suita, Japan.
Manager Hajime Moriyasu made five changes to the side that beat Tajikistan 4-1 a week ago and opted for Onaiwu to lead the attack in the absence of Takumi Minamino, who withdrew from the squad last week "due to club circumstances".
With qualification already secured, Minamino, who had netted in all seven of Japan's previous group matches, reportedly left after playing in the 1-0 friendly win against Serbia on Thursday, to sort out a move from Liverpool to Southampton.
In his place, Onaiwu opened the scoring from the penalty spot in the 27th minute after a handball by Aizar Akmatov.
Onaiwu tapped in his second four minutes later at the far post after good work down the right by Kawabe Hayao and completed his quickfire treble in the 33rd minute with a towering header.
Takuma Asano and Sho Sasaki added two more after the break while Kyrgyz captain Mirlan Murzaev scored their consolation penalty in first-half stoppage time.
In the other Group F match, Tajikistan beat Myanmar 4-0 in Osaka to seal second place.