Penaud scored the opening try of the match in only the second minute, touching down without a hand laid on him as France moved the ball quickly from an attacking scrum. Fullback Melvyn Jaminet kicked the conversion, the first of his 17 points in the match.
Japan rallied with a try to Samoa-born flanker Tevita Tatafu while flyhalf Seungsin Lee matched Jaminet's conversion and two penalties before halftime.
Japan had a major setback when regular flyhalf Takuya Yamasawa tested positive for Covid-19 on the day before the match, leaving Lee to take over the No 10 jersey.
Matthis Lebel scored France's first try of the second half when Japan centre Dylan Riley was impeded in defence and Penaud scored his second in the 57th minute. Jaminet converted both and added a penalty before Yoram Moefana collected a kick behind the defense and touched down. By that point France had scored 22 unanswered points in as many minutes.
A try to Pierre Bourgarit in the 69th minute snuffed out any chance of a late Japan revival, though the home side scored the final try of the match through Siosaia Fifita.
France had only a handful of players who featured in their last Six Nations match against England and coach Fabien Galthie likely will be pleased with the performance of his young and experimental lineup.
The teams meet again next weekend.
- AP