The result gave South Korea back-to-back titles, after K-League rivals Pohang Steelers won the competition last year, and booked Seongnam's place in December's Club World Cup.
An ebullient Shin promptly indulged in a Jose Mourinho-like boast after the game in Tokyo.
"I'm double-happy to be Asian champions as a coach after winning it as a player," said a beaming Shin who played for the 1995 side.
The 40-year-old told reporters he was still haunted by Seongnam's previous appearance in the AFC Champions League final in 2004.
He watched both legs from the bench as Ilhwa beat Saudi Arabia's Al Ittihad 3-1 away before suffering a stunning 5-0 home humiliation which cost the club the title.
"I've tried not to let those bad memories linger," said Shin. "It's like mind control, trying to banish those ghosts but we did it so I can say I am a 'special one' too now."
Seongnam took the lead in the 29th minute when Australian captain Sasa Ognenovski bundled the ball into the net following a goal-line scramble.
A free kick from Seongnam's Colombian striker Uribe Molina near the corner flag almost crept in before Zobahan forward Mohammad Ghazi forced a smart save from South Korea's World Cup goalkeeper Jung Sung-ryong just before halftime.
Seongnam, last Asian champions in 1995, made it 2-0 seven minutes into the second half when defender Cho Byung-kuk headed in from close range.
Striker Mohammadreza Khalatbari pulled a goal back for Zobahan in the 67th minute but Kim Cheol-ho stabbed in a third for Seongnam eight minutes from time to seal victory.
"We made too many mistakes," said Zobahan coach Mansour Ebrahimzadeh. "We gave away two silly goals. The players were in tears but life goes on and they have to learn from it.
"Nobody gave Zobahan a hope in this competition but we've finished as runners-up and made people notice us. At least people know our name now."
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