Tokyo were looking to make it three home wins on the bounce, but they went into half-time trailing after when Shingo Hyodo opened the scoring in the 31st minute at the Ajinomoto Stadium.
Yokohama were met with stubborn resistance in the second half, but former Celtic midfielder Shunsuke Nakamura notched his sixth goal of the season to wrap up the three points in the final minute.
It means Yasuhiro Higuchi's side now top the J.League as Sanfrecce Hiroshima were held 1-1 at home by Nagoya Grampus courtesy of an injury-time leveller from Marcus Tanaka.
With the game looking like it was heading for a goalless draw, Mihael Mikic finally broke the deadlock at the EDION Stadium in the 77th minute.
The home fans thought that goal would be enough to give their side maximum points, but they were denied by Tanaka's late strike.
Urawa Reds maintained their position in the AFC Champions League positions after an amazing comeback saw them turn around a three-goal deficit against bottom side Oita Trinita to win 4-3 at the Saitama Stadium 2002.
Goals from Yohei Kajiyama, Masashi Wakasa and Riki Matsuda saw the away side storm into a comfortable lead after 20 minutes, but Shinzo Koroki reduced the gap before half-time.
And the second half was dominated by Urawa, as a Marcio Richardes strike and an own goal from former Leicester City midfielder Yuki Abe levelled the game.
And the comeback was complete with just six minutes remaining when defender Daisuke Nasu secured the points for Mihailo Petrovic's side.
In the battle between two sides in the relegation zone, Shonan Bellmare were held to a 1-1 draw by Jubilo Iwata.
The home side had Wellington Sousa to thank for gaining what could be an invalubale point, as his equaliser cancelled out Yuichi Komano's opener.
Elsewhere, Cerezo Osaka romped to a 4-1 victory over Shimizu S-Pulse, while there were also home victories for Sagan Tosu and Kashima Antlers. The former triumphed 2-1 over Omiya Ardija, while the latter secured a 1-0 success over Albirex Niigata.
Kawasaki Frontale were successful on their travels, as they earned a 3-1 win over Ventforet Kofu, and the match between Kashiwa Reysol and Vegalta Sendai ended 0-0.
