In Townsville on Saturday, the coaches squared off for the second time in seven days.
Next time they meet could be in the round-of-16 at the World Cup in Australia next year.
The Wallabies came from 17-14 down to win 56-17 and complete a series sweep after a tense 35-32 Osaka win in Kiss's first game in charge.
Jones, who coached Australia to the final of the 2003 World Cup on home soil, made a controversial return to Japan after a failed cameo with the Wallabies that included an historic early exit from the 2023 showpiece.
He lasted less than a year into a five-year contract that was designed to keep him in charge for another home Cup next year.
Instead there's every chance his Japan face the Wallabies in a spicy knockout clash, should both teams finish second in their groups once action starts next October.
"The headline was 'the Wallabies will be like rabbits in headlights', when we played New Zealand in the semi-final when we beat them," Jones recalled of the 2003 experience.
"There was this wave of negativity around the team and then it just turns and you've got this positivity.
"And there's no greater experience than coaching your own team in a home World Cup.
"Les has started well. He'd be happy with those couple of wins and I wish him all the best apart from when he plays us again."
Jones lamented the second-half blowout in Townsville, when the hosts began to win high balls and slowly grind down a Japan side that had until that point had a reply to every Australian blow.
But with world-class lock Warner Dearns, a swathe of Australian expats including fellow second-rower Harry Hockings and a host of emerging local stars, there is hope the world No.12 side can make some noise on their next visit to the country.
"Being an Australian, coaching against Australia is one of the greatest honours you can have in rugby," Jones said after the defeat.
"We've played three good halves of rugby against Australia ... but have 10 blokes under 10 caps, so sustaining that effort when you're not getting immediate reward is difficult.
"It's a great, difficult experience."
Jones blooded three university students who are yet to play professionally at club level, including livewire flyhalf Ryunosuke Ito who recently signed with Suntory.
"We've got to go and bow and ask the university if we can have him (for Tests later this year)," Jones said.
"It's a unique situation ... back to university Monday, train with 150 players, one coach, one physio.
"So hopefully we'll have a good experience with the university lecturers."
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