By FOX Sports staff
Having played out a 0-0 draw in last week's first leg in China, Seoul were dealt a blow at the Seoul World Cup Stadium after just nine minutes when Frederic Kanoute pounced on a defensive error to fire Beijing into the lead and hand them a priceless goal.
The hosts then wasted an excellent chance to equalise on the hour mark when Dejan Damjanovic fired his penalty back off the post, but they were not to be denied a minute later when Adilson was left with a simple tap-in after a mix-up between Xu Yunlong and Yang Zhi.
Yun Il-lok then fired Seoul ahead in the 70th minute with an emphatic finish and the closing stages were marred by red cards to Adilson and Beijing duo Kanoute and Zhang Xinxin, before Koh Myong-jin added a third in injury-time to seal his side's progress.
Speaking after the game, Choi revealed he always had faith his side would be able to get the job done.
"Our performance in the second half was remarkable," he said on the AFC's official website.
"We were 1-0 down in the first half but I always believed in the players."
The 39-year-old will now turn his attentions to preparing his side for the quarter-final stage and insists his players are not lacking in any motivation to win Asia's premier club competition.
"We have a lot of experienced players and we have a lot of excellent technical players," Choi added. "And the chance to become Asian champions motivates these players even more.
"The big challenge begins now and we will prepare well to ensure we finish on top."
Despite the defeat, Beijing boss Aleksandar Stanojevic believes there were plenty of positives to take from their performances this season and claimed there was little difference between them and their conquerors over the 180 minutes.
"FC Seoul made us of home advantage and I can't blame the players," he said. "I was forced into making some substitutions due to injuries but after that we had some mistakes and the players were unable to respond.
"Our last league game also affected the players but overall it is a good experience for the young players.
"We wanted to make history but we were unsuccessful even though there was not a big difference between ourselves and FC Seoul."
And having seen his side fall agonisingly shot in reaching the last eight of the competition for the first time ever, the Serbian is determined to lead them back amongst the continent's elite next year.
"We were close to qualifying for the quarter-finals, which would have been our best achievement in the AFC Champions League," Stanojevic added. "But we showed what we are capable of and we are not far behind the Korean teams.
"We will now concentrate on the league and challenge again in the 2014 AFC Champions League."
Seoul will find out who their quarter-final opponents are on June 20 when the draw is made.