
Yokohama, last season’s runners-up, went into the home leg with a 1-0 lead from the opening fixture in China and they put themselves further in front with two goals in the opening half hour.
Shanghai pulled one back but Yokohama scored again before halftime before adding another after the break.
The win earned Yokohama, coached by Gareth Southgate’s former England assistant Steve Holland, a place in the AFC Champions League Elite final tournament in Saudi Arabia.
Games will be played over 11 days in Jeddah, with the quarterfinals kicking off on April 25.
Yokohama made a dream start on a drizzly evening when a Shanghai defensive mix-up set up their opening goal just over a minute after kickoff.
Asahi Uenaka threaded the ball through to Daiya Tono and the striker buried it past goalkeeper Yan Junling.
Tono hit the post soon after as Yokohama kept up the pressure and Anderson Lopes doubled their lead a minute short of the half-hour mark.
Midfielder Kodjo Aziangbe cut through the Shanghai defence before slipping the ball through to Lopes, who beat Yan with a cute finish.
Shanghai gave themselves a chance when Brazilian Leonardo turned home a flick-on from captain Li Ang to pull one back five minutes later.
But Yan Matheus restored Yokohama’s cushion with their third goal minutes from halftime after another quick break forward.
Lopes hit his second goal 10 minutes after the break after Aziangbe had thumped the post.
It was the top-scoring Brazilian’s ninth goal of the competition.