Sanfrecce trailed at half-time to a Yu Kobayashi goal but Hisato Sato drew them level in the 57th minute before Tsukasa Shiotani snatched a 90th-minute clincher after Jeci had been sent off for the visitors.
The result leaves Sanfrecce as one of four teams boasting 100 per cent records from the opening two rounds, with Kashima Antlers, Sagan Tosu and last season's runners-up Yokohama F. Marinos also enjoying perfect starts.
Kashima and Sagan both sit atop the table with identical goal differences of plus six, with Sanfrecce fourth behind Marinos, who were 1-0 victors over Shimizu S-Pulse thanks to Manabu Saito's 13th-minute goal. Shimizu had Kota Sugiyama sent off in the 77th minute.
At the other end of the table, three teams are still looking for their first point - including second-bottom Vegalta.
Tokushima Vortis prop up the standings after losing 2-0 at home to Cerezo Osaka, a 10th-minute Hotaru Yamaguchi strike and a Mitsuru Chiyotanda own goal three minutes later settling that match, while third-bottom Omiya Ardija lost 2-1 at home to Nagoya Grampus Eight.
Nagoya scored twice through Keiji Tamada (53) and Yoshizumi Ogawa (66) to take control, and Omiya could only pull one goal back through Shohei Takahashi 20 minutes from time.
In other matches, Gamba Osaka defeated Albirex Niigata 2-0 with goals from Keisuke Iwashita (69) and Kotaro Omori (82), while the games between FC Tokyo-Vantforet Kofu and Vissel Kobe-Kashiwa Reysol both finished 1-1.
FC Tokyo took a fifth-minute lead through Edu but were pegged back by Cristiano Da Silva's 72nd-minute leveller, and in Kobe, hosts Vissel wiped out Wataru Hashimoto's 45th-minute opener with a Junior equaliser just after the hour, but their hopes of pushing on for the win were hit by the 76th-minute dismissal of Simplicio.