Forward Cho Dong-Keon struck the only goal in the 30th minute, allowing the South Koreans to tighten up their defence for the remainder of the game. The result made the tie 4-4 on aggregate, but the Koreans went through by virtue of having scored more away goals.
It was sweet revenge for the seven-time K-League champions, who led three times in the first leg through spectacular volleys by Mauricio Molina and Jo Jae-Cheol before conceding two late goals to lose 4-3 two weeks ago.
Uruguayan Jose Manuel Olivera was the hero for Al Shabab in the first leg in Riyadh with a brace, while club captain Abdoh Autef made a decisive impact as a 70th-minute substitute, helping to set up the third and fourth goals respectively.
Seongnam reached the semi-finals three years ago and last the final of the competition in 2004, when they lost to Jeddah giants Al Ittihad over two legs.
The Koreans will meet Zob Ahan in the final on 13 November in Tokyo after the Iranian club stunned Saudi Arabia powerhouse Al Hilal, later in the evening. The Iran Pro League leaders secured a maiden berth in the continental decider with a 1-0 victory in Riyadh thanks to a lone strike from Igor Castro for a 2-0 aggregate semi-final scoreline.