An own goal from Kosuke Kikuchi set Sanfrecce on their way after 24 minutes before the home side pulled level through Zlatan Ljubijankic's penalty seven minutes before the interval.
Kohei Shimizu's goal four minutes into the second half proved decisive though, as Sanfrecce moved two points clear of a Vegalta side who fell to a surprise 2-1 loss at lowly Consadole Sapporo.
The points appeared to be going Vegalta's way when Kodai Watanabe scored after 12 minutes, but a Takuma Hidaka strike after 79 minutes levelled the scores before Watanabe put through his own net in the final minute to gift a third win of the season to basement side Consadole.
Kashiwa Reysol lie five points behind the leaders following a 1-1 draw against FC Tokyo. Lucas fired the home side in front after 11 minutes but that was cancelled out by Jorge Wagner in the 68th minute.
Urawa Red Diamonds lost ground at the top with a 1-0 defeat to Vissel Kobe, the only goal coming from Yoshito Okubo via the penalty spot.
Struggling Gamba Osaka picked up a welcome point in a 2-2 draw at home to Cerezo Osaka.
Two goals from Takuma Edamura gave Cerezo the edge but Gamba responded with a brace from Akihiro Sato.
Morais Renato Caja and Yasushi Endoh were on target in a 2-1 win for Kashima Antlers over Jubilo Iwata, who went ahead early on through Ryoichi Maeda.
Sagan Tosu were also 2-1 winners over Kawasaki Frontale. The home side went in front with a goal from Kengo Nakamura, but a Yuki Saneto own goal and a strike from Yohei Toyoda turned things around.
Shohei Abe put through his own net while Toshiyuki Takagi and Genki Omae were also on target as Shimizu S-Pulse edged out Nagoya Grampus Eight 3-2.
Taishi Taguchi and Cordoba Danilson were the scorers for Nagoya.
Yuji Nakazawa scored twice and Marcos Marquinhos added another to seal a 3-2 win for Yokohama F. Marinos at the expense of Albirex Niigata, for whom Atomu Tanaka's brace was not enough.