Leandro Domingues' brace twice got the hosts back on level terms, but when Shingo Akamine put Vegalta ahead for the third time 12 minutes from time Kashiwa had no response.
Naoki Sugai had opened the scoring in the second minute, with Kunimitsu Sekiguchi (56) putting them ahead for the second time soon after Domingues' first equaliser.
The win kept the leaders three points clear of second-placed Urawa Red Diamonds and third-spotted Nagoya Grampus Eight, who both enjoyed comfortable wins.
Second-half strikes from Yuki Abe and Marcio Richardes earned Urawa a 2-0 triumph at Vissel Kobe, while Nagoya saw off bottom-of-the-table Consadole Sapporo 3-1 - Mu Kanazaki, a Tatsuki Nara own goal and Keiji Tamada on the scoresheet for the hosts before Hiroyuki Furuta's last-minute consolation.
Elsewhere, struggling Gamba Osaka battled from two goals down to pick up their first win of the season - 3-2 against Kawasaki Frontale.
Kawasaki were two up after half an hour through goals from Yusuke Tasaka and Yu Kobayashi, but Gamba - who had managed only one point from five previous games - stunned their visitors by turning the game on its head courtesy of efforts from Sota Nakazawa, None Sato and Hiroyuki Sato.
Yasushi Endoh snatched a last-gasp winner for second-bottom Kashima Antlers as they too collected their first three-point haul of the campaign by prevailing 2-1 at FC Tokyo.
Sotan Tanabe looked to have grabbed a point for the capital club when his 84th-minute goal cancelled out Shinzo Koroki's opener, but Endoh had other ideas.
Genki Omae's brace helped Shimizu S-Pulse come from behind to edge Jubilo Iwata 3-2.
Toshiyuki Takagi scored S-Pulse's first on the stroke of half-time to make it 1-1 at the break after Byung-Kuk Cho's 12th-minute opener, before Omae took centre-stage after the interval to put the game out of reach. Kosuke Yamamoto reduced the deficit in the dying seconds but it was not enough.
An 82nd-minute equaliser from Yu Hasegawa ensured Omiya Ardija a 1-1 draw at Yokohama F Marinos after Yuji Ono had put the home team ahead eight minutes into the second half.
Finally, Kisho Yano grabbed the winner five minutes from time to clinch a 1-0 victory for Albirex Niigata at Cerezo Osaka.