Karne Hesketh's stoppage-time try clinched a 34-32 triumph over the Springboks to record the biggest World Cup shock of all time and truly ignite this year's tournament.
Jones, who admits he thought his side would put up a fight for 60 minutes but was not sure they could win, was taken aback as he walked down to the pitch at the Amex Stadium to congratulate his players.
"When we got down to pitch level it seemed as if everyone was crying. I've never seen more grown men in tears. It was an absolutely unbelievable scene which will live with me for the rest of my life," he said in the Daily Mail.
"I'll never cease to wonder at the Japanese psyche. These guys seem to cry when they're happy and laugh when they're nervous - it's almost the opposite of Western behaviour - and the tears were flooding out on the pitch. It was an amazing place to be."
Former Australia coach Jones admits that when Japan had a penalty in South African territory late on - with the score at 32-29 in the Boks' favour - he tried to get the message down to his charges to kick for goal and go for a draw.
But skipper Michael Leitch - who was outstanding throughout - had already made the call to go for it and push for a try to win. Jones ended up being delighted his instructions fell on deaf ears.
"The lift this will give rugby in Japan and the World Cup as a whole is incomprehensible. It showed that an upset of this magnitude - a top three team in the world beaten by one from outside the top 10 - is possible," he added.
Jones' former rival Sir Clive Woodward, whose England side beat Jones' Australia in the 2003 World Cup final, has described Japan's victory as the "greatest single rugby moment in World Cup history".
Woodward, also writing in the Daily Mail, said: "It was a performance of breath-taking brilliance and courage and also a coaching coup of thrilling panache which sends out a message to the entire sporting world, not just rugby. Underdogs can become world beaters if you truly believe."