Star forwards Messi, Neymar and Kylian Mbappe all started for PSG in front of a crowd of 65,000 at Tokyo’s National Stadium.
Messi opened the scoring in the 32nd minute but a much-changed PSG line-up in the second half could manage only one more goal through substitute Arnaud Kalimuendo.
J-League champions Kawasaki pulled a goal back in the 84th minute when Kazuya Yamamura headed home unmarked.
New PSG manager Christophe Galtier, who has arrived from Nice, was happy with the workout against a team in the middle of their domestic season.
“There were some good phases of play and some good combinations in attack,” he said.
“I liked the way we were able to put them under pressure high up the pitch, which led to some dangerous chances.”
Mbappe was denied several times by goalkeeper Jung Sung-ryong in the first half after combining well with Messi.
The Argentine had a shot cleared off the line but gave PSG the lead soon after when he guided a shot into the corner from just inside the box.
Kawasaki gave the European heavyweights plenty of problems and Galtier said his defence would have to shape up before the new season.
“We gave away far too many chances in front of our goal,” he said.
“This is where we have the most work to do. We have to keep the right balance and adjust more quickly to these transition situations.”
PSG will play two more J-League sides, taking on Urawa Reds in Saitama on Saturday and Gamba Osaka in Osaka the following Monday.
The game against Kawasaki was played in energy-sapping humidity and PSG midfielder Vitinha said the heat took its toll.
“We are not used to the weather — it’s difficult because it’s very hot and we feel it in the field,” said the Portuguese, who arrived this summer from Porto.
“It’s physically hard but it’s not an excuse. We are going to be more prepared and well prepared for the upcoming games.”
Neymar and Mbappe departed at half-time and Messi bowed out soon after as Galtier rang the changes.
Substitute Kalimuendo doubled PSG’s lead when he turned home Juan Bernat’s low cross in the 58th minute, before Yamamura pulled one back with six minutes to play.