Goals from Asahi Uenaka and Jun Amano in four second-half minutes earned Steve Holland's side victory in Pudong Stadium but the line-up for next month's knockout rounds remains uncertain after Shandong pulled out of the competition.
The withdrawal, which Shandong claimed was due to health issues within their squad, was announced by the Asian Football Confederation hours before the Chinese side were due to face South Korea's Ulsan HD in their final match.
Shandong's decision to pull out should mean all of the club's results in this season's tournament are annulled as per the competition's regulations.
That has cast an air of uncertainty over the final league phase table for east Asia.
If Shandong's results are expunged, three clubs -- Buriram United, Shanghai Shenhua and Shanghai Port -- have earned points across eight matches compared to seven for the remaining teams in the competition.
The AFC has said the matter will be referred to the relevant committees "as appropriate for their decisions".
No timeline has been given. First leg ties are regarding due to be played early March.
The uncertainty had no bearing on Yokohama's performance as last season's runners-up dominated in Shanghai.
Home goalkeeper Yan Junling made a string of saves to deny the Japanese club until Uenaka thumped a rising shot beyond the goalkeeper in the 64th minute.
Amano doubled the lead four minutes later when he chested in Kanta Inoue's cross from the right to earn Marinos a deserved victory.
That put Marinos top of the table, a status they should retain even if their draw with Shandong is expunged.
