Japan matched France physically in the first half in Tokyo on Saturday and trailed 28-15 at halftime, but lost touch on the scoreboard after conceding two tries early in the second.
It was a successful three-week tour for the Six Nations champion France, who were coming off a 42-26 win over Australia in Brisbane last week after opening the new 12-team tournament with a 34-32 loss to the All Blacks in New Zealand.
Japan finished the first phase of the Nations Championship with consecutive losses to Ireland and France after opening the tournament with a 27-10 win over Italy.
At the National Stadium in Tokyo, the French opened the scoring in the second minute when hooker Lamothe drove over after a close-range lineout.
Japan gained a one-point lead with fullback Takuro Matsunaga kicking a penalty goal, then sparking a long-range counter-attacking try from his own quarter line that was finished in the left corner by winger Kippei Ishida in the 15th minute.
France regained the ascendancy over the next 20 minutes, rebounding with tries to fullback Jalibert in the 19th minute after sustained forward pressure - which resulted in a yellow card for Japan lock Harry Hockings - and No.8 Alexandre Roumat in the 23rd minute.
Skipper and scrumhalf Lucu darted over after a strong run into contact from his hooker Lamothe and touched down on the half-hour mark to score France's fourth try, securing a bonus competition point.
After narrowly missing a try in the right corner, Japan cut the margin to 13 points with a try four minutes before the break.
France scored early again in the second half, with Jalibert scoring in the 43rd when he changed running angles and took a short pass on Lucu's inside shoulder and crossed near the posts.
Lamothe scored again in the 51st minute, after sustained forward pressure from the big French pack. It was 42-15 and a much bigger margin seemed ominous.
But Jalibert was yellow-carded for a high tackle in the 58th minute and, although Japan weren't able to turn the one-man advantage into a try in the 10 minutes, it stopped France's momentum.
Japan had a try disallowed in the 63rd minute and didn't score in the second half on a hot and humid evening.
