Former Japan international Nakamura struck the only goal of the game after just four minutes to help Yokohama earn their first win in three league matches.
Behind them, defending champions Sanfrecce Hiroshima ended a run of three successive defeats with a 2-0 home triumph over Albirex Niigata, Hwang Seok-ho opening the scoring after 28 minutes and Hisato Sato adding a second just eight minutes later.
That victory saw Sanfrecce climb into second spot, level on 47 points with Urawa Red Diamonds who were held 1-1 at home by Vantforet Kofu.
Urawa were just moments away from claiming all three points through a 51st-minute Yuki Abe penalty but they could not hold as Naoaki Aoyama struck a last-gasp leveller for improving Vantforet.
Kashima Antlers are three points further back in fourth place following their 3-2 win at second-bottom Jubilo Iwata.
Goals from Shoma Doi (four minutes), Davi (62) and Takahide Umebachi (75) put Kashima in total control and despite being forced to suffer a nervy finish after seeing Jubilo pull goals back through Baek Sung-dong (81) and Yoshiro Abe (90), the visitors held on for the spoils.
Fifth-placed FC Tokyo picked up a third consecutive win as goals from Aria Jasuru Hasegawa (38) and Nemanja Vucicevic (88) fired them to a 2-0 win at Nagoya Grampus Eight, while Vegalta Sendai won by the same scoreline at Omiya Ardija, Naoki Ishikawa (53) and Ryang Yong-gi (73) the men on target.
Elsewhere, a 68th-minute strike from Takashi Kanai saw Sagan Tosu defeat Kawasaki Frontale 1-0 while Shonan Bellmare were 2-1 winners at Oita Trinita thanks to a Kosuke Taketomi brace.
Taketomi scored in the 15th and 54th minutes to sandwich a 41st-minute equaliser from Yu Yasukawa.