Matsumoto appeared on course for an unlikely goalless draw after some profligate Reds finishing and solid saves by keeper Tomohiko Murayama, before the defender's curling left-foot shot from the edge of the penalty area nestled in the top corner.
The 1-0 victory took the Reds to 10 points from four games, two clear of FC Tokyo and Vegalta Sendai, who also both won on Saturday.
Hirofumi Watanabe struck a 95th minute effort to give Vegalta a 2-1 success over Shimizu S-Pulse and also stay unbeaten this season, while Tokyo were 1-0 winners over Ventforet Kofu after an early goal from Naohiro Ishikawa.
Kawasaki Frontale are one of four teams tied on seven points after two goals by former Japan striker Yoshito Okubo in the second half completed a 4-1 win over Albirex Niigata.
Holders Gamba Osaka are also on seven points after their 3-1 success over winless Nagoya Grampus Eight on Friday briefly took them ahead of the Reds.
Sanfrecce Hiroshima can join the Reds at the top on 10 points if they beat bottom club Vissel Kobe later on Saturday.