Striker Cho Dong-keun got the all important goal to end what has been a disappointing season for Seongnam on a high leaving Suwon, looking for a third straight victory in the competition, to focus on the first leg of their AFC Champions League semi-final at home to Al Sadd on Tuesday.
The game was heading for extra-time in wet conditions at Tancheon Stadium but the deadlock was broken with 14 minutes remaining of a hard-fought game.
Hong Chul's corner was aimed at the near post and Cho was on hand to head the ball past goalkeeper Jung Song-ryeong to win Seongnam's first FA Cup since 1999.
"It is a great feeling to win the FA Cup, especially after the final two years ago," said Seongnam coach Shin Tae-yong, referring to 2009 when Seongnam lost a penalty shoot-out to Suwon.
"Of course we are happy to be back in the AFC Champions League after winning it last year."
Suwon boss Yoon Sung-hyo at least has the consolation of focusing on other competitions.
"We are down because we think that the FA Cup is very important," he said.
"Congratulations to Seongnam for their win and thanks to our fans who came to give us lots of support. If our luck had been different we could have won but now we will focus on the AFC Champions league and the semi-final next week."