Vissel Kobe had a chance to pull off the upset win but a late extra time goal from Junior was enough to send Ulsan through to the finals.
Junior Negrao's brace sent Ulsan through where they will face a Vissel squad that barely eked out a win over Suwon.
Former champions Ulsan will face Beijing while Kobe's quarterfinal debut will be against two-time title holders Suwon.
Vissel's passage to the quarterfinals may have come at a cost while Suwon shocked Yokohama with a comeback win.
Guangzhou Evergrande could have sealed a knockout berth with a win over Suwon but will now need help from Vissel.
Guangzhou made gains in Group G by topping Vissel , while Shanghai SIPG dropped Yokohama Marinos for their first loss of the tournament.
Andres Iniesta was brilliant as Vissel Kobe secured passage to the knockout rounds with a win over Guangzhou Evergrande.
With the East Zone set to return, Andres Iniesta, Ki Sung-yueng and Rhyan Grant will be key as their sides seek to reach the finals.
Vissel Kobe have told fans not to sing, chant or wave flags in their season-opening clash with Yokohama FC due to the spread of coronavirus.
Vissel Kobe and Yokohama F Marinos missed nine consecutive spot kicks in the deciding penalty shootout as Andres Iniesta's team eventually won.
Former Barcelona and Spain striker David Villa has announced he will retire at the end of the year.
Spain's World Cup-winning striker Fernando Torres ended a glittering 18-year career on Friday with his final match for J-League club Sagan Tosu.
Carles Perez scored twice as Barcelona beat a Vissel Kobe side including Andres Iniesta 2-0 in the Rakuten Cup on Saturday in Japan.
Sergi Samper, who has made one appearance this season, said his desire to play regular football again was the main reason behind his decision.
Andres Iniesta has said he and his family struggled to adapt after swapping Barcelona for Vissel Kobe but they are now beginning to feel settled.
Andres Iniesta released a statement explaining a social media post that prompted criticism because of a photo that included two people in blackface.
Andres Iniesta has been criticized on social media for posting a photo showing him with a group of people, including two in blackface.
David Villa has revealed that he will be joining up with former Spain teammate Andres Iniesta in Japan at Vissel Kobe, after leaving NYCFC.
Andres Iniesta, now at Vissel Kobe, said he had struggled in the months following Barcelona's 2008-09 success.
Andres Iniesta is to have a monument dedicated to him in his home province of Albacete in tribute to his stellar contribution to the Spanish region.
Club said Shunki Takahashi had told a friend via instant messaging that Iniesta, who joined in May, would not appear against Urawa Reds on Sept. 23.
Andres Iniesta is soon to be the star of his very own fly-on-the-wall television series covering his transfer to Vissel Kobe.
Sagan Tosu won 3-0 with Torres scoring the third goal after 84 minutes.
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