The 2003 champions Al Ain also reached the last four with a 1-0 win at Lokomotiv Tashkent and will face either Al Nasr and El Jaish, who meet later on Wednesday.
Shandong's Walter Montillo opened the scoring by heading home Hao Junmin's cross on the hour to shock the 2013 finalists at the Jinan Olympic Sports Centre.
However, Yun Ju-tae equalised for Seoul seven minutes from time, ending the hosts' chances of reaching their first Asian Champions League semi-final.
Shandong came out all guns blazing from the start, with Italian striker Graziano Pelle, who joined the club from English Premier League side Southampton in July, drawing a save from goalkeeper Yu Sang-hun in the fifth minute.
Shandong's Zhang Chi missed one of the best chances to break the deadlock by hitting the side netting two minutes later.
Seoul's Park Chu-young nearly made Shandong pay for their missed opportunities when he found himself free on goal midway through the first half, only to be denied by keeper Wang Dalei.
(Reporting by Ian Rodricks in Bengaluru; Editing by Ken Ferris)
