Messi, 35, suffered his lowest-scoring league tally since 2005-06 last season, scoring just six goals in Ligue 1. The Argentina forward scored 11 in all competitions.
Messi fired home PSG's opening goal against Kawasaki with a right-footed, deflected effort after being teed up by Achraf Hakimi.
Arnaud Kalimuendo added to the scoring in the second half by firing past Sung-Ryong Jung from close-range after a neat move.
Kawasaki scored six minutes from time to reduce the arrears as Kazuya Yamamura beat substitute goalkeeper Sergio Rico with a header.
Messi was one of five substitutions made in the 62nd minute. Teammates Mbappe and Neymar were swapped out after half-time as Christophe Galtier eased his side back to match fitness.