Goals from Lee Jae-sung and Oh Hyeong-gu gave underfire coach Hong Myung-bo his second win in a row and lifted the Koreans on to seven points from three matches.
Hong had been booed after Korea's opening 0-0 draw with Palestine in Seoul but back-to-back wins mean the Taeguk Warriors are in a strong position to continue their record of qualifying for every World Cup since 1986.
A header from Lee gave South Korea, missing injured captain Son Heung-min, the lead in the 38th minute and Oh doubled the advantage 23 minutes into the second half when he wrong-footed Yazeed Abulaila to score from inside the area.
In Group A, Uzbekistan were unable to find a way past Iran's defense despite the visitors having only 10 players for the final 35 minutes of their top-of-the-table clash as they played out a 0-0 draw in Tashkent.
Defender Saleh Hardani was shown a red card 10 minutes into the second half for a dangerous tackle on Uzbekistan captain Eldor Shomurodov.
The top two in each group advance automatically to the World Cup while the third and fourth-placed sides go into another round of preliminaries.