The fast-starting Japanese, coached by former Wallabies and England boss Jones, were worn down by Fiji at Hanazono Stadium with weight and speed and with impact off the bench, scoring five tries — two more were disallowed — for a record-extending sixth PNC title, and first since 2018.
"A couple of our young guys today struggled with the occasion," Australian Jones said.
"Unfortunately the only way to learn from that is to have it, and I'm sure they're going to be better for it."
After early penalty kicks, Japan centre Dylan Riley scored a brilliant solo try by cutting inside three defenders and collecting his own chip.
Counterpart Inia Tabuavou then had a try chalked off by a knock-on in the buildup, but Fiji eventually tied the score against the run of play when wing Vuate Karawalevu touched down.
Fiji started the new half with a man advantage while Japan hooker Mamoru Harada was sin-binned. Standout flyhalf Caleb Muntz had a try disallowed because of obstruction but his 56th- minute penalty gave Fiji the lead for the first time.
Replacement Ponepati Loganimasi then finished a try on his test debut and a minute later, Fiji were in again through replacement forward Albert Tuisue.
Fiji crossed twice more in the next eight minutes, Loganimasi's offload released Karawalevu for his second try, then Loganimasi broke from a midfield ruck and stepped the last defender for try number two.
Muntz kicked six from six and let Isaiah Armstrong-Ravula convert their last try.
Tuitama gave Japan some consolation with the last converted try but the hosts lost to Fiji for the sixth time in their last seven contests.
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