Goals in either half from Shunsuke Nakamara that flanked Marcos Marquinhos' strike on 29 minutes saw Yokohama take advantage of Hiroshima's 2-0 defeat to Vantforet Kofu.
The 15th-placed club pulled off the shock win thanks to goals from Yoshifumi Kashiwa (eight) and Kazunari Hosaka (52).
Cerezo Osaka are in fourth place behind Urawa after salvaging a 1-1 draw at Vegalta Sendai. Takahiro Ogihara's goal on the stroke of half-time earned a point following Ryang Yong-gi's opener.
There were seven goals in Shizuoka as Shimizu S-Pulse edged a 4-3 win over Kashima Antlers.
The visitors took an early two-goal lead through Yuya Osako and Kazuya Yamamura but Shimizu levelled before the break thanks to Dzenan Radoncic and Toshiyuki Takagi.
Takagi added another shortly after the interval and, just after Osako had scored his second with an 88th-minute penalty, he wrapped up a hat-trick and all three points for the hosts.
Another high-scoring encounter saw Kashiwa Reysol beat Shonan Bellmare 5-2 in Chiba - Masato Kudo and Kenta Kano both bagging braces for the hosts.
Elsewhere, Albirex Niigata beat Jubilo Iwata 4-2 while Sagan Tosu claimed a 3-2 win at FC Tokyo.
Kawasaki Frontale triumphed 2-1 over 10-man Omiya Ardija, for whom Zlatan Ljubijankic was sent off, and Nagoya Grampus Eight defeated Oita Trinita by the same scoreline.