Sasa Ognenovski opened the scoring in the first-half before Cho Byung-kuk's 52nd minute goal had Seongnam cruising.
Mohammadreza Khalatbari threatened to spark a late Zob Ahan fight-back when he headed home in the 66th minute but Kim Cheol-ho grabbed a third for Seongnam with eight minutes remaining to ensure the AFC Champions League trophy remains in Korea Republic following Pohang Steelers' triumph last year.
Seongnam had been slow to start and it took until the 14th minute for them to register their first effort when Song Ho-young's clever ball unlocked the Zob Ahan defence and allowed Mauricio Molina to race through on goal, but the Colombian forward drove his shot wide of the right post.
Ognenovski prevented Zob Ahan from taking the lead in the 24th minute after keeper Jung Sung-ryong weakly punched Mahdi Rajabzadeh's free-kick straight to Igor Castro but the Brazilian's goal-bound shot was headed off the line by the Seongnam skipper.
It was a crucial intervention as just five minutes later Ognenovski gave Seongnam the lead.
Kim Sung-hwan's long throw caused havoc in the box and when Zob Ahan were unable to clear, Ognenovski took advantage to prod home from close range.
That goal sparked a period of Seongnam dominance and the Zob Ahan defence had to be at their best to prevent the Koreans from extending their lead before the break.
But the Iranians almost snatched an equaliser seconds before half time when Ghasem Hadadifar's cross from the left found Mohammad Hosseini inside the area but the right-back's close-range shot on the turn was expertly turned around the post by Jung.
Seongnam came out strong after the restart with the lively Molina causing Zob Ahan all sorts of problems and Shahab Gordan needed to push his low drive behind for a corner in the 51st minute.
But it was from the resulting set piece that Seongnam extended their lead when Cho Dong-geon flicked the ball on for Cho Byung-kuk and the defender directed a deft header into the back of the net.
Zob Ahan halved the deficit with 24 minutes remaining, however, when Igor Castro stabbed a shot that deflected off Jung to Khalatbari, who looped a smart header over backtracking defenders and into the empty net.
Jung protected Seongnam's slender advantage with little over 10 minutes remaining, blocking Hadadifar's shot at the near post and it seemed only a matter of time before Zob Ahan would find an equaliser.
But Seongnam secured Asian club football's most coveted trophy in the 82nd minute when Molina's shot struck a defender and Kim Cheol-ho was on hand to collect the ball and fire home