Port lost 2-0 in their final league phase match to the Japanese club on Wednesday in Shanghai but have progressed as a result of the withdrawal of compatriots Shandong Taishan.
Shanghai's place in the next round was ratified by the AFC's publication of the official fixture list for the last 16.
Marinos, who topped the 12-team east Asian league standings, will travel to face Port in the first leg on March 4th. Thailand's Buriram United will host Johor Darul Ta'zim of Malaysia on the same day with the return fixtures played a week later.
Shanghai Shenhua will entertain Japan's Kawasaki Frontale and reigning J-League champions Vissel Kobe will host South Korea's Gwangju FC in their first leg fixtures on March 5th, with the second legs on March 12th.
The winners of the four ties will advance to the quarter-finals, where they will join the four qualifiers from the west of the confederation in a centralised finals in Jeddah in Saudi Arabia from April 25th to May 3rd.
On that side of the draw, Cristiano Ronaldo's Al Nassr will take on Esteghlal from Iran while Al Sadd from Qatar meet Al Wasl of the United Arab Emirates on March 3rd and 10th.
Four-time champions Al Hilal face Uzbekistan's Pakhtakor while their fellow Saudis Al Ahli play Qatar's Al Rayyan on March 4th and 11th.
Shandong pulled out of Wednesday's meeting with South Korea's Ulsan HD citing health issues and the withdrawal saw their results expunged from the tournament records.
Under the tournament's regulations, Shandong face a minimum $50,000 fine, a suspension of at least one season from AFC competitions plus the return of all subsidies received.
The club could also be made to pay compensation to cover losses incurred by rival clubs and commercial entities with a decision due to be made by the AFC's disciplinary and ethics committee.