Two goals in either half were enough to see the leaders extend their advantage by another point as rivals Sagan Tosu and Kashima Antlers suffered surprise defeats to struggling sides.
Ryota Moriwaki and Tadanari Lee netted within six minutes of each other midway through the first half to put the league leaders ahead at the break.
Tomoaki Makino added a third with 18 minutes to play before Yasuhiro Hiraoka pulled a goal back for S-Pulse, but any sense of consolation was wiped out as he put through his own goal late in the game.
Tosu's patchy league form continued against relegation battlers Ventforet Kofu as they were beaten 1-0.
Veteran defender Kohei Morita scored the only goal of the game on Saturday as Megumu Yoshida's men fell to their third defeat in five league matches.
Antlers suffered their first defeat in the league since May as Omiya Ardija ended a 10-game winless run with a 2-1 victory.
Shohei Takahashi was the Ardija hero as he struck the winning goal in the 74th minute after Dragan Mrda's opener had been cancelled out by Gen Shoji.
Kawasaki Frontale took full advantage as they moved into second place with a comprehensive 4-0 victory over bottom club Tokushima Vortis.
They were ahead after just five minutes thanks to An Byong-jun, with Yu Kobayashi striking his 10th league goal of the season in first-half stoppage-time.
Renatinho and Jeci compounded Vortis' misery with two goals in seven minutes just after the hour to ensure Frontale leapfrogged both Tosu and Antlers.
Cerezo Osaka ensured there is only two points between four sides in the bottom half as they beat Kashiwa Reysol 2-0, while Vegalta Sendai were beaten 1-0 by Albirex Niigata.
Elsewhere, there were also wins for Nagoya Grampus and Gamba Osaka but Tokyo were denied all three points as Vissel Kobe came from a goal down to draw 1-1.
