Brazilian Jorginho opened the scoring for Seongnam midway through the first-half and Huang Bowen got the equaliser three minutes before half-time.
In the 96th minute Kim Do-heon scored with a penalty to give the home side the win.
The visitors started well with Ricardo Goulart and midfielder Huang shooting wide inside the first 10 minutes.
Seongnam should have taken the lead after 10 minutes as Jorginho got control of the ball after a defensive error by Mei Fang only to hammer his shot straight at goalkeeper Zeng Cheng.
Guangzhou kept creating chances as Yu Hanchao, Zhao Xuri and Goulart all threatened to score for the visitors.
For the home side Nam Joon-jae wasted a great chance after failing to direct his header from Ricardo Bueno's deep cross on target.
In the 23rd minute Guangzhou goalkeeper Zeng was beaten when Kim Do-heon passed the ball to Jorginho inside the area and he scored with a low shot to make the score 1-0.
Guangzhou were back on level terms three minutes before half-time as Huang scored with a stunning shot from 30-yards beating goalkeeper Park Jun-huk.
During the second half both sides attacked but there were few clear-cut chances.
Guangzhou had defender Li red-carded in the 65th minute following a high-footed challenge on Ricardo Bueno.
After the red-card Seongnam seemed to have the upper hand and came close to scoring via Ricardo Bueno and Jung Seon-ho.
In the 96th minute Kim Do-heon squeezed his dramatic spot kick past Zeng to hand Kim Hak-bum's side the advantage in the tie.