Fellaini headed in the first goal from a corner in the 30th minute and Graziano Pelle added the second in the 39th. Safawi Rasid scored for Johor in the 59th. Shandong Luneng is in second place in Group E, while Johor is last.
In the other group match, defending champion Kashima Antlers came back from a two-goal deficit to beat South Korea club Gyeongnam 3-2. Takeshi Kanamori and Serginho both scored in injury time to keep Kashima in first place in the group.
Cedric Bakambu scored a hat trick to give Beijing Guoan a 3-1 win at Thai club Buriram United.
The Democratic Republic of Congo international scored two goals in the first 30 minutes and added the third in the second half.
It was Beijing's first victory in three matches in Group G.
In the other group match, South Korean club Jeonbuk Motors moved into first place by beating Japanese team Urawa Reds 1-0.
Brazilian striker Adriano scored the lone goal in the 77th minute.
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