A Naoki Ishihara brace for the visitors was enough to secure back-to-back title wins for Sanfrecce after Yokohama lost their final game to complete a late-season slump.
Yokohama had looked set to seal the crown in comfortable fashion after taking a five-point advantage over the eventual winners into the final two matches, but Yasuhiro Higuchi's men failed to take a point from either game.
Sanfrecce's victory, coupled with Yokohama's 1-0 defeat at Kawasaki Frontale, ensured the title will remain at the EDION Stadium.
Kawasaki's triumph was their fourth league win in a row and their remarkable recent form guaranteed their place in next season's AFC Champions League, with Kashima's defeat having denied them a spot.
Cerezo Osaka also missed out on the top three but denied Urawa Reds the honour by beating them 5-2, with Yoichiro Kakitani scoring his 20th and 21st league goals of the season in the win.
The defeat was the Reds' third in a row and left them sixth in the final table, when the summit had been in their sights approaching the run-in.
At the bottom, the relegated sides had already been condemned, with Shonan Bellmare continuing their poor recent form as they were beaten 1-0 by Omiya Ardija.
Shonan have lost their last six top-flight matches, while Jubilo Iwata beat fellow relegated side Oita Trinita 3-1.
Kengo Kawamata scored in Albirex Niigata's 2-0 win over Nagoya Grampus but will have to settle for second place in the scoring charts behind Kawasaki's Yoshito Okubo, who ended the season with 26 league goals.
Kashiwa Reysol came from a goal down to beat Shimizu S-Pulse 2-1 while second-half goals from Lucas and Sota Hirayama handed Tokyo victory over Vegalta Sendai.
The league's lowest scorers Ventforet Kofu drew a blank against Sagan Tosu in the only goalless game of the weekend.
