Mauricio Molina, Asian player of the year Sasa Ognenovski, Choi Sung-Kuk and Cho Dong-Geon were all on target with Fernando Baiano hitting the Gulf team's consolation.
The South Koreans were ahead after just four minutes when a mix-up between Hamdan Al Kamali and goalkeeper Adel Al Hosani allowed Colombian midfielder Molina to score into the unguarded net from 20 yards.
Al Wahda were level on 27 minutes when Baiano headed Eisa Ahmed’s cross beyond goalkeeper Jung Sung-Ryong.
But Seongnam were back in front on the half-hour mark when their Australian captain Ognenovski headed in from six yards.
That became 3-1 with 19 minutes remaining when an unmarked Choi Sung-Kuk scored following some good work from Cho Dong-Geon.
Cho added the fourth, heading in a Molina cross beyond Al Hosani.
Seongham Ilhwa will face Inter Milan on Wednesday with Internacional of Brazil tackling African champions Tout Puissant Mazembe on Tuesday in the first semi-final.