The Thai League 1 champions advanced at the Malaysians' expense when Suphanat Mueanta scored the only goal in Johor to earn Osmar Loss' team a 1-0 win on the night and overall.
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.
The results mean Marinos and Buriram United advance to the finals phase of the competition, which will be played in Jeddah from April 25th to May 3rd.
"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.
"Very happy for them because they deserve it."
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 after their defender Li Ang glanced Mateus Vital's corner towards goal to give them a lifeline in the 35th minute only for Yan Matheus to restore the Japanese side's two-goal cushion.
The Brazilian bent his left-foot shot around Yan into the bottom corner with a minute left in the first half to leave the Chinese club with little hope going into the second period.
Lopes put the result beyond doubt 11 minutes after the break when he converted from close range having seen Kodjo Aziangbe's shot from distance rattle Yan's right post.
Buriram United, meanwhile, qualified for the last eight for the first time since 2013 with Suphanat scoring the only goal in a keenly contested tie between the Southeast Asian rivals.
The teams went into the second leg level having shared a scoreless encounter in Thailand last week and there was nothing between the sides again in the opening 45 minutes in Johor.
The game shifted Buriram's way 13 minutes into the second half, however, when Suphanat curled a left-foot shot beyond Andoni Zubiaurre into the top corner to send the Thais through.