Hosts Kawasaki went ahead through Yu Kobayashi after 20 minutes, before Vegalta levelled four minutes later when Shingo Tomita netted. The league frontrunners inched ahead after 54 minutes thanks to Rodrigues Wilson, but Vegalta were back on level terms in the 61st minute when Kyohei Noborizato replied.
And Yajima provided the dramatic finish by pouncing for the winner in the 90th minute.
Sanfrecce Hiroshima closed to two points behind Vegalta - who have 27 points from 13 games - thanks to a 3-1 win at bottom side Consadole Sappora, with goals from Hisato Sato (21), Satoru Yamagishi (27) and Koji Morisaki (83) - the reply coming from Yoshihiro Uchimura (50).
Jubilo Iwata stand a point further back after a 4-0 home success over Omiya Ardija, with a double from Ryoichi Maeda and further goals from Hiroki Yamada and Takuyo Matsuura doing the damage.
Shimizu S-Pulse were held 0-0 at home by Yokohama F Marinos, while FC Tokyo drew 1-1 with Urawa Red Diamonds. Marcio Richardes put Urawa ahead after 88 minutes but Masato Morishige grabbed a late equaliser.
Kashiwa Reysol overcame Albirez Niigata 2-0 with an own goal from Masaaki Higashiguchi in the 32nd minute followed by a further effort from Masakatsu Sawa four minutes from the end.
Kashima Antlers were 2-1 winners at Vissel Kobe, as goals from Juninho (7) and Shinzo Koroki (51) put them in charge before Yuzo Tashiro replied in the last minute.