He produced some history as well as they became the first Asian nation to reach eight consecutive World Cups, co-hosting in 2002 among those appearances.
These are the types of games Clarke wants his players to pit their wits in, against opponents they seldom get the chance to face, with Ivory Coast next on Tuesday.
This match is also important to the visitors as they prepare for games against the Netherlands and Tunisia in the summer, with a further European nation joining them from the play-offs for their games in Arlington and Guadalupe.
Japan are without three star men for the game at Hampden, in Real Sociedad winger Takefusa Kubo and Monaco's former Liverpool midfielder Takumi Minamino - who are both long-term injured - as well as former Arsenal defender Takehiro Tomiyasu, now of Ajax.
However, there is still plenty for Clarke to concern himself with as they look to win a Hampden friendly for the first time in a decade, as noted by Brighton & Hove Albion's Kaoru Mitoma, who is arguably the star turn in Japan squad.
"I think we've certainly made people take notice by becoming the fastest nation to qualify, but if we want to take that next step, there's still a lot of things we need to do," the winger said on that memorable night in Saitama.
"If we want to win the World Cup, we need to improve our attack, improve our defence, improve plenty of things and there's still a wall in front of us, but we will do all we can to get over that."

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