Thai champions Buriram United also advanced at the expense of Malaysia's Johor Darul Ta'zim.
The pair join Ronaldo's Saudi club Al Nassr and Qatar's Al-Sadd in the last eight.
Lopes' brace in Yokohama took him top of the tournament's scoring charts with nine goals and sent Steve Holland's Marinos side on their way to a victory that secured a 5-1 aggregate win.
"Very happy with the performance, very happy with the result and very happy that the players get the chance to play in an exciting knockout competition in Saudi at the end of April," said Holland, referring to the finals phase, which will be played in Jeddah from April 25 to May 3.
Leading 1-0 after the first leg, Daiya Tono extended Marinos' overall advantage with less than two minutes on the clock when he crashed a left-foot shot past Yan Junling and Lopes doubled the lead in the 29th minute with a dinked finish.
Shanghai Port's Leonardo pounced to score from close range in the 35th minute only for Yan Matheus to restore the Japanese side's three-goal aggregate cushion.
Lopes added a finishing touch 11 minutes after the break when he converted from close range.
Buriram United qualified for the last eight for the first time since 2013 with Suphanat Mueanta scoring the only goal in Johor to earn a 1-0 win on the night and overall.
Al Nassr and Al-Sadd reached the quarter-finals on Monday. Later on Tuesday (local time) in Saudi Arabia Al-Hilal and Al-Ahli will seek to, respectively, overturn Uzbek club Pakhtakor's 1-0 first-leg lead and defend a 3-1 advantage over Qatar's Al-Rayyan.
On Wednesday Shanghai Shenhua take a 1-0 lead to Kawasaki Frontale and Vissel Kobe defend an 2-0 advantage at Gwangju.
