The win over South Africa was lauded as Japan's 'coming of age' as a rugby nation by pundits worldwide, but Jones was far less bullish about the 2019 World Cup hosts' prospects.
"The legacy now is how the Japan Rugby Football Union uses the win and how strong they are in developing good coaching systems and improving infrastructure to go forward," the 55-year-old Australian told Kyodo News at Japan's team base in Warwick, England.
"This is like a balloon. It can be popped or it can be a real growth spurt. It's entirely the responsibility of the JRFU.
"To keep improving, things have to change. I couldn't go back after the World Cup and do what I have done for the last four years because we are not going to improve enough within the current structures. I know enough about rugby to know that."
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Jones, who coached Australia to the 2003 World Cup final, said the Brave Blossoms were not just a representative team of Japan's top players, but also had to act as a development team and a casualty ward for their injured.
"We've had to use it for rehab and keep injured players with us because we can't send them back (to their domestic teams)," he said.
"All those things have to change if Japan wants to be a serious rugby country.
"One of the reasons I decided not to continue was because I didn't think those things could change."
After four years in charge, Jones will quit Japan after the World Cup to coach the Cape Town-based Stormers in the southern hemisphere's Super Rugby competition.
His departure has also means he won't take up an appointment as director of Japan's fledgling Super Rugby team which is to join an expanded 18-team competition next season.
The new team is still unnamed, lacks a coach and has yet to unveil a playing list but Super Rugby's governing body SANZAR confirmed it in the draw for the 2016 season released on Monday.
"I am surprised Super Rugby is going ahead (with them) but maybe there were legal ramifications," Jones said.
"It just hasn't got the right infrastructure in place to be successful and it could end up doing more harm than good."
(Reporting by Ian Ransom in Melbourne; Editing by Julian Linden)
