Lee, who scored twice on Saturday in a 3-0 friendly win over Uzbekistan, made it four goals in two games with a strike in each half against a poor UAE team.
South Korea now have four points from their opening two games in Group Two while UAE look dead and buried and pointless with three defeats from three games.
As expected the hosts attacked from the beginning at Seoul World Cup Stadium.
Just after Park Ji-sung shot wide, Zenit St Petersburg defender Kim Dong-jin managed to guide a close range headed past the UAE post. Lee Keun-ho should have opened the scoring after 18 minutes.
The in-form Daegu star broke free of the UAE defence but shot straight at Majed Naser in the UAE goal. Two minutes later however, he made amends. Latching on to a finely measured through pass from Lee Chung-young, Lee fired past Majed Naser in the UAE goal.
The stadium was on its feet five minutes later as the new captain showed what he has learned at the home of the English and European champions.
On the edge of the area, Park beat a UAE defender to a Lee Young-pyo pass, turned his man and lashed the ball into the top corner.
The visitors threatened only intermittently but almost pulled a goal back just before the break as Korean defender Cho Yong-hyung’s clearance from a corner only just cleared the crossbar.
The second half started in much the same fashion as the first and six minutes in, Ki Sung-yeung showed why he is one of Asia’s hottest properties –almost. Spying Naser off his line, the FC Seoul midfielder’s attempted 20-yard lob bounced off the crossbar.
UAE’s defence was battling to stay afloat in a sea of red and it seemed that it was only a matter of time before a third came.
It almost did on the hour, Kim Hyeung-bom saw his free-kick turned over the bar by a flying Naser. The keeper was beaten from the resultant corner but a defender was on hand to clear Kim Dong-jin’s header off the line.
Unbelievably, South Korea handed UAE a lifeline with 19 minutes remaining. Defender Cho Yong-hyung, under pressure from substitute Ismail Salem, chose to try and dribble his way out of trouble but succeeded only in losing possession as Salem went on to round the keeper and score.
Lee calmed any nerves with a fine finish from just inside the area to seal the win and with two minutes remaining, defender Kwak Tae-hwi headed home a fourth.