The draw was enough to secure Marcello Lippi's side the trophy on away goals, after a 2-2 draw in the first leg, with the Chinese Super League champions completing a domestic and Asian double.
Evergrande also became the first Chinese club to win an Asian title in 23 years and the first from their country to win the competition in its current format.
After a low-key first half, the game's only goals came within 16 minutes of the second half starting, Elkeson giving the home side the lead three minutes before the hour.
While Dejan Damjanovic equalised shortly after, it was not enough, as Lippi became the first manager to win UEFA and AFC Champions League titles.
Dario Conca went close for the hosts after 15 minutes, hitting the post with an effort after Zhang Linpeng produced a cutback from the right byline.
Two minutes into the second half, Evergrande threatened again, but Kim Yong-Dae saved well from Muriqui's close-range effort before the goalkeeper made himself equal to Huang Bowen's strike from outside the area.
Ha Dae Sung almost put the visitors ahead seven minutes before the hour mark, with a chip that needed to be touched over by Zeng Cheng.
However, Seoul's limited amount of threat was punished by Brazilian Elkeson, who slotted home after taking Muriqui's through ball in his stride after 57 minutes.
It was the Brazilian's third goal in two matches, after clinching a brace in his side's final Chinese Super League game of the season on Sunday - a 5-0 win over Wuhan Zall.
The lead lasted just four minutes however, when Damjanovic expertly turned a Sergio Escudero pass home, after dribbling well to carve out an opportunity.
However, the visitors were unable to carve out any further chances as Evergrande finished the competition unbeaten at home.
