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Terry Antonis of Melbourne Victory clears during the AFC Champions League match against Shanghai SIPG
Heading into the final round of the group games, Melbourne had already been eliminated.
But the A-League team inflicted a first defeat in the tournament on the big-spending Chinese Super League team that finished on top of Group G.
Pierce Waring put Melbourne ahead after 40 minutes with Lin Chuangyi making it 1-1 just before the break for a Shanghai team that started without star Brazilians Hulk and Oscar.
Jai Wingham hit the winning goal midway through the second half.
Ulsan Horangi of South Korea took the second spot, joining Shanghai in the round of 16, and drew 2-2 with bottom team Kawasaki Frontale of Japan.
Melbourne ended the tournament in third as did fellow Australia team Sydney FC the previous evening,
Jeonbuk Hyundai Motors finished top of Group E after defeating Kitchee of Hong Kong 3-0 in South Korea, a fifth win in six games.
The two-time winners had to wait until the second half to break the deadlock with Lee Seung-gi getting the first and Kim Shin-wook heading home the second. Lim Seon-yong scored the third.
Tianjin Quanjian of China, making a debut appearance in the tournament, finished in second after a 3-2 win over Kashiwa Reysol of Japan.
Two first-half goals from Zhao Xuri put Tianjin ahead with Yang Xu finding the net on the second half.
Kashiwa finish third in the group with Kitchee in fourth.
Both legs of the second round will be played in May.
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