Shingo Hyodo scored the only goal after 63 minutes to ensure Yokohama stay out in front on goal difference ahead of Kashiwa Reysol, who were 2-1 winners over Kashima Antlers.
Kashiwa went ahead at home after 33 minutes through Hideaki Kitajima, but Yuzo Tashiro equalised for the visitors 12 minutes into the second half.
Leandro Domingues made sure of the points for Kashiwa, though, with his strike 10 minutes from time.
Nagoya Grampus Eight beat Sanfrecce Hiroshima 3-2 to remain four points behind the top two.
Although they trailed to Tadanari Lee's sixth-minute goal, Nagoya equalised after 15 minutes through Marcus Tanaka and were gifted the lead in the 68th minute thanks to an own goal from Kohei Morita.
Takahiro Masukawa then fired home 10 minutes from time to give the hosts a 3-1 lead, with Toshihiro Aoyama's goal coming too late for Hiroshima.
Fourth-placed Kawasaki Frontale lost ground on the leaders with a 1-0 defeat at Albirex Niigata, Bruno Lopes netting after 53 minutes.
Gamba Osaka twice threw away the lead in their match with Jubilo Iwata, eventually settling for a 2-2 draw.
Satoshi Yamaguchi's seventh-minute opener for hosts Gamba was cancelled out by Hidetaka Kanazono after 37 minutes.
Lee Keun-ho then restored Gamba's lead 10 minutes into the second half but they were once again frustrated by a 70th-minute equaliser from Hiroki Yamada.
Kim Bo-kyung scored twice as Cerezo Osaka hammered Shimizu S-Pulse 4-0.
Kim scored in the 54th and 79th minutes to sandwich a penalty from Shu Kurata (59). Takashi Inui then rounded off the result in the final minute.
Urawa Red Diamonds were 2-0 winners over strugglers Vantforet Kofu, with Tadaaki Hirakawa (53) and Yosuke Kashiwagi (73) on the scoresheet.
Lee Chun-soo netted in the 53rd minute to earn Omiya Ardija a 1-0 victory at Vegalta Sendai.