Japan's Gamba Osaka also booked a last 16 place after their 2-1 victory over Seongnam FC of South Korea who had already qualified.
Suwon Bluwings and FC Seoul are the two other K-League sides to have booked their place for the knockout stage starting on May 19.
Lee Jae-sung's 25th minute header put Jeonbuk ahead but Shandong equalised through Wang Tong before halftime.
Kim Hyung-il, Eninho and Edu struck for the hosts after the break as Jeonbuk finished second in Group E behind Kashiwa Reysol of Japan.
In Group F, Osaka trailed at halftime after Hwang Ui-jo's 15th minute strike put two-time Asian champions Seongnam ahead but the J-League side hit back in the second half.
Birthday boy Takashi Usami equalised for the 2008 winners in the 64th minute before Brazilian forward Lins scored with eight minutes remaining to send them through to last 16 as the group winners.
Thai Premier League side Buriram United blanked bottom placed Guangzhou R&F 5-0 to join Osaka and Seongnam on 10 points but lost out on head-to-head record. (Reporting by Amlan Chakraborty in New Delhi; editing by Justin Palmer)