Japan put in their best performance under coach Jamie Joseph on Saturday as they beat Tonga 39-6 at Stade Ernest Wallon.

Going up against a side that qualified for the 2019 Rugby World Cup as the second-ranked team from Oceania behind Fiji, the Brave Blossoms blew the Pacific islanders away with some scintillating 15-man rugby and a well-organized, robust defense.

Japan came into the game as the more experienced side with their starting XV having won 392 caps to Tonga's 157, while the benches saw more of the same with Japan's replacements having played 58 tests to just six by Tonga's reserves.

And it was experienced campaigners such as captain Michael Leitch, Keita Inagaki and Yu Tamura alongside newcomers such as Wimpie van der Walt, Kazuki Himeno and man-of-the-match Lomano Lava Lemeki who were at the heart of the Japanese effort.

"That was a really physical game, a step up from the game against Australia," said Lemeki, who scored two of Japan's five tries.

The influence of new defense coach John Plumtree was also very evident as Japan stopped wave after wave of attacks from their bigger opponents.

"We have been working a lot with John and implementing his system," said Leitch. "And it is finally starting to come right."

Japan got off to a perfect start with Lemeki going over in just the third minute after the forwards had laid the platform with a good driving maul.

Sonatane Takulua closed the gap with a penalty five minutes later but that only saw Japan lift their game, aided by some missed tackles from the Tongans.

Tamura added a penalty to his earlier conversion as Japan restored their seven-point advantage.

But with Japan's line-out struggling and their discipline at the breakdown upsetting referee Andrew Brace, Tonga once again closed the gap through the boot of Takulua.

However, it was indiscipline from Tonga that proved to be the turning point.

With lock Halaleva Fifita sent to the sin bin in the 28th minute, Japan scored two tries in quick succession through Amanaki Lelei Mafi and Leitch.

And with Tamura converting both tries and adding a second penalty the Brave Blossoms led 27-6 at the break.

The second half was a more even affair as both coaches took the opportunity to blood players off the bench.

Replacement scrumhalf Yutaka Nagare prevented a certain Tonga five-pointer with a good tackle before Lemeki added his second try in the 60th minute following some more good work from the pack and a clever inside pass from Tamura.

Kenki Fukuoka closed out the scoring with a try in the 74th minute as he used his pace to beat the Tongan cover defense as Japan recorded their biggest ever winning margin over the 'Ikale Tahi.

"Poor execution in attack and defense" was the reason given by Tonga captain Takulua for the loss.

"We couldn't get our set piece going and slipped off too many tackles."

Japan take on France next week in a battle between the nations hosting the next two Rugby World Cups.

And as Leitch pointed out, the Brave Blossoms will need to recover quickly from their defensive heroics.

"The body is sore," he said. "All 23 Japan players will be feeling it today."