Muscat announced last week he was leaving after two-and-a-half years at the club and goals from Elber, Anderson Lopes and Yan Matheus gave Marinos the win they needed to top Group G and qualify automatically for the next round.
Shandong joined Yokohama in the last 16 despite losing to their hosts, Choi Kang-hee's team pipping South Korea's Incheon United to second place in the group with 12 points enough to claim one of the three best runners-up slots.
The Chinese team progressed despite Incheon's 3-1 win over Kaya FC from the Philippines in the other game in Group G, with that result meaning the top three teams in the group all accumulated the same number of points.
Yokohama topped the group due to their better head-to-head goal difference over Shandong and Incheon, with the same metric ensuring the Chinese side finished second.
Muscat's team started the game in Yokohama in third place in the standings and, needing a win to progress, opened the scoring in first-half stoppage time when Elber slipped between defenders to steer Matheus' through ball past Wang Dalei.
Anderson Lopes doubled the lead from close range 12 minutes into the second and Matheus completed the win in style seven minutes later with a brilliant lob on the run over the stranded Wang.
In Group F, Jeonbuk came back from going behind to an early Wanchai Jarunongkran goal to defeat already-qualified Bangkok United 3-2 and confirm themselves as another of the three best runners-up.
Jeonbuk's win ended Melbourne City's hopes of qualification for the last 16, with the Australians joining defending champions Urawa Red Diamonds as one of two group runners-up to miss out.
Wanchai put the visitors in front with four minutes on the clock but Moon Seon-min levelled a minute before the interval.
Two goals in two minutes from Lee Dong-jin won the tie for Dan Petrescu's side, despite Rungrath Phumichantuk's late second for Bangkok United.
Yokohama, Shandong, Ulsan and Jeonbuk join a last-16 line-up that also features Japan's Ventforet Kofu and Kawasaki Frontale as well as Bangkok United and Pohang Steelers in the eastern half of the draw.
Saudi Pro League quartet Al Nassr, Al Hilal, Al Ittihad and Al Feiha have qualified in the west alongside Uzbekistan's Nasaf Qarshi and Navbahor Namangan as well as Al Ain of the United Arab Emirates and Sepahan from Iran.
The draw for the next round will be held on December 28th with the first leg of the last 16 scheduled to be played on February 12th-14th with the return fixtures on February 26th-28th.
