Japan coach Eddie Jones his team's fairytale run at the Rugby World Cup after admitting the Asian minnow was a "joke" before the tournament.

Japan's remarkable World Cup campaign closed with a 28-18 victory over United States on Monday (AEDT).

Jones's team exited the tournament with three wins from four games, after producing the biggest upset in rugby union history to stun two-time champion South Africa in their Pool B opener.

Japan narrowly missed out on a quarter-final berth behind Scotland but Jones was still proud of his players as they became the first team in history to be knocked out at the pool stage after claiming three victories.

"It's disappointing but look, we had a great World Cup," Jones said. "We played as well as we can today, down to our last resources, and USA kept coming, so the win tonight was a pretty good effort.

"It's been fantastic, we've only got one starting Super [Rugby] player in our squad, so the guys have all played above themselves, worked hard, with spirit, and played how rugby should be played." 

Japan had only ever won one World Cup match prior to this year's tournament in England/Wales.

That rare win came in 1991, when Hiroaki Shukuzawa's men downed Zimbabwe 52-8.

Japan had also conceded combined scores of 184, 210, 163, 140 and 252 at the past five World Cups.

But that all changed in 2015 as Japan earned a place in rugby folklore thanks to its memorable opening 34-32 win against the Springboks last month.

A 26-5 victory at the expense of Samoa in game three was to follow as Japan bowed out of the World Cup with just 100 points conceded, while it scored 98 of its own.

"Let's be honest, before this tournament Japan were one of the joke teams," Jones said. "Teams would put out their B team against them and win by 80-90 points.

"To come here and win three out of four games is a super effort from the team. It shows how hard they have worked to achieve this."