Katsuya Nagato had been sent off for a second bookable offence two minutes into the second half in Yokohama for a Marinos side that held a slender 2-1 lead over the Chinese side from the first leg last week.
But Lopes' 75th-minute strike gave the Japanese a two-goal cushion overall and Gao Zhunyi's sending off with seven minutes remaining eased Yokohama's path to the next round.
Marinos will face Ulsan Hyundai in the semi-finals on April 17th and 24th after Hong Myung-Bo's side saw off fellow South Korean side Jeonbuk Motors with a 2-1 aggregate win in their semi-final on Tuesday.
"I'm glad it's over," said Kewell. "We worked hard over the two legs.
"They're a very difficult team, they play direct, they're big, they're strong.
"I don't think we helped ourselves but we got the job done. We created enough chances, especially in the first part of the game, to bury it."
Marinos will be playing in the semi-finals for the first time in the club's history and were rarely troubled by a Shandong side needing to score to keep alive their hopes of progressing.
After a tight first half, the complexion of the game changed when Nagato was sent off in the 47th minute for a foul on Tong Lei having picked up his first booking just before halftime.
Li Yuanyi went close to levelling the overall score on the hour mark, lifting the ball over the goal from close range after William Popp had kept out the midfielder's initial effort.
Marinos continued to attack despite being shorthanded and Lopes struck with 15 minutes remaining, cracking in a left-foot volley from Riku Yamane's lofted pass.
Gao's dismissal for taking down Ryo Miyaichi snuffed out Shandong's hopes of finding a way back into the tie and Marinos progressed to complete the semi-final line-up.
In west Asia, Al Hilal from Saudi Arabia will face Al Ain of the United Arab Emirates having seen off compatriots Al Ittihad on Tuesday.
Al Ain, meanwhile, eliminated Cristiano Ronaldo's Al Nassr on Monday.
