The Montenegro striker, who got Seoul's goal in the first-leg 1-1 draw, got the only goal of the second leg with seconds remaining as they advanced with a 2-1 aggregate win.
Iranian champions Esteghal are also through after a 2-1 win away to Buriram United completed a 3-1 aggregate victory.
Buriram levelled the tie when Osmar Barba headed them in front on the night in the 38th minute.
But Hanif Omranzadeh restored Esteghal's advantage early in the second half and Andranik Teymourian's long-range effort sealed it late on.
Over at the Abdullah bin Khalifa Stadium, Chinese giants Guangzhou Evergrande produced a majestic display to beat Qatari side Lekhwiya 4-1 and progress 6-1 on aggregate.
After Dario Conca had fired the visitors ahead in the 14th minute, Elkeson doubled their lead just two minutes later before Muriqui added a third a minute after the half-hour mark to put the result beyond doubt.
Lekhwiya did pull one back six minutes after the break when Zhang Linpeng scored an own-goal, but it was Evergrande who had the last say as they rounded off the scoring in the 77th minute when Elkeson grabbed his second of the night.
Finally, J.League outfit Kashiwa Reysol became the final team to book their place in the last four on away goals following a 3-3 aggregate draw with Saudi Arabia's Al Shabab.
With the scores level at 1-1 from last month's first leg, it was the hosts who took the lead at the King Fahd International Stadium in the 10th minute when Naif Hazazi netted, only for Ryoichi Kurisawa to equalise three minutes later.
Kashiwa then went ahead and grabbed a vital second away goal in the 73rd minute through a Naoya Kondo effort, which proved to be crucial as Al Shabab equalised on the night five minutes from time when Hassan Muath Fallatah found the back of the net, but it proved to be not enough for the Saudis.
Wednesday's AFC Champions League Quarter-final Results
FC Seoul 1-0 Al Ahli (2-1 on agg.)
Buriram United 1-2 Esteghlal (1-3 on agg.)
Lekhwiya 1-4 Guangzhou Evergrande (1-6 on agg.)
Al Shabab 2-2 Kashiwa Reysol (3-3 on agg., Kashiwa on away goals)