The win moves the UAE into second place in Group G on 12 points, 2 points behind Vietnam who breezed past Indonesia with a 4-0 win.
It also means Thailand are now unable to capture second spot in the group which would ensure qualification to
The UAE had a 2-0 lead before half-time courtesy of goals from naturalised Brazilians Caio and Fabio de Lima.
The War Elephants were handed a glimmer of hope when 18-year-old striker Suphanat Mueanta pulled one back after the break, before Mohammed Jumaa scored a late third for the UAE to put the result beyond doubt.
Thailand sit in third place in the group on 9 points after seven games; the UAE and Vietnam have both played six games each. Next up for Thailand is the game against Malaysia on June 15 (kick off 11.45pm Phuket time).
Elsewhere, Syria confirmed their position at the top of Group A with a 3-0 win over Guam. The result sees Syria join Japan in the third round of qualifying where they will be among the 12 teams competing in the next phase for four confirmed spots from Asia in next year’s tournament in Qatar.
Japan defeated Tajikistan 4-1 earlier in the day in Group F to secure their place in the next round with Liverpool striker Takumi Minamino scoring for a seventh consecutive match, equalling the national record set by Keisuke Honda in the process.
Also in Group A, China defeated the Philippines 2-0 although they remain 8 points behind Syria and can only hope to qualify as one of the best second placed teams throughout the groups.
In Group B, Australia hammered Taiwan 5-1 to maintain top spot on 18 points while Uzbekistan stayed in contention in Group D after trouncing Singapore 5-0 and now sit 2 points behind leaders Saudi Arabia.
Iraq trounced Cambodia 4-1 in Group C to remain top. Iran are 2 points behind them in second after defeating Bahrain 3-0.
At the end of the second qualifying stage, eight group winners and four best second-placed will make it to the final phase of the Asian qualifiers.