
The Japanese side faced a tense second half at Yokohama International Stadium when Katsuya Nagato was sent off two minutes after the break with his team only a goal ahead on aggregate.
But Anderson Lopes scored in the 75th minute to settle the nerves and take former Leeds and Liverpool forward Kewell’s side into their first Champions League semifinal.
They will play South Korea’s two-time Asian champions Ulsan Hyundai next month for a place in the final.
Shandong also finished the match with 10 men after Gao Zhunyi was sent off in the 83rd minute.
Yokohama took a two-goal lead in last week’s quarterfinal first leg in China but conceded in the 91st minute to let Shandong back into contention.
Shandong’s Brazilian striker Cryzan, the competition’s joint-top scorer with eight goals, started the first leg on the bench but he was named in the line-up for the return fixture.
He was a constant thorn in Yokohama’s side and Yan Matheus had to make a crucial intervention to head clear with the striker lurking midway through the first half.
Yokohama were forced into a change shortly before half-time when Matheus left the match on a stretcher.
And the home side were reduced to 10 men just minutes into the second half when Nagato was shown a second yellow card for a foul on defender Tong Lei.
Shandong began to press the advantage and Li Yuanyi should have done better when he shot over the bar after goalkeeper William Popp had kept out his first effort.
Lopes settled the matter with Yokohama’s goal 15 minutes from time, volleying home Riku Yamane’s cross with a sweet left-foot finish.
Ulsan beat fellow South Koreans Jeonbuk 1-0 in yesterday’s quarterfinal second leg to advance to the semis 2-1 on aggregate.