Kuwait's 2-0 defeat to South Korea meant Lebanon progressed to the next stage of the qualifying process, finishing as runners-up behind South Korea in their four-team group.
That progress had seemed unlikely as Lebanon stood 146th in the FIFA rankings, the lowest of the 20 teams going into the third round.
Coach Emile Rustom resigned on the eve of the campaign after four months in the role, to be replaced by Theo Bucker, the German taking charge of the Lebanese national team for the second time, 11 years after his first stint.
"Looking at our opponents in the group nobody believed we would be in a position to step through to the next round," Bucker told reporters on Wednesday.
"This match today showed us our weak points and now we have three to four months to work on this in order to show a better face when we continue this competition."
Lebanon are one of 10 teams who will play the fourth round in two pools of five, with the top two in each pool qualifying for the 2014 finals in Brazil while the third-placed sides will play off against each other, with the winners playing the fifth-ranked South American side.
Lebanon went into Wednesday's match knowing they would guarantee progress by avoiding defeat.
They were backed by thousands of passionate supporters who turned half the Al Nahyan Stadium in Abu Dhabi into a sea of red. With the UAE having no chance to qualify, the other half of the stadium was almost empty.
A goalkeeping error by Abbas Hassan, who dropped a free-kick from Basheer Saeed into his net after 20 minutes, allowed UAE to go a goal up.
Lebanon equalised two minutes later when Mahmoud Al Ali burst through to score but he injured himself in the process and had to be replaced.
Ali Al Wehaibi restored the UAE's advantage eight minutes before the interval, only for his side to be pegged back once more when Hassan Maatouk equalised in stoppage-time.
The second half saw the UAE take control with Ismail Matar and Saeed scoring with long-range strikes.
