Suwon Bluewings stayed on course for their first Champions League title since the competition was launched in its current format in 2003.
Brazilian Erik gave the Marinos a 1-0 lead at the break with a 20th minute strike, but the Koreans were a different team altogether after the break.
They struck through Kim Tae-Hwan to draw level in the 57th minute and towards the end of play upped their tempo to go 3-1 ahead with goals from Kim Min-woo and Han Suk-jong in the final 10 minutes.
A strike by Ado Onaiwu in the first minute of stoppage time added to the tension but Park Kun-ha's side held on to seal their spot in the next phase.
"Yokohama's press and speed in the first half took us by storm but we grew in confidence later. I want to thank our players and the fans in Korea who stayed up late to watch the match", said Park.
Standout matches today