With a beer in one hand, he spoke about the "outstanding" performance of the team - who were wearing medals presented in light of their success.
The duke said: "I genuinely think rugby has the ability to unite everyone around the world and I could not think of a nation that needs it more than [South Africa] right now."
Harry's message of unity is one being celebrated in the Springbok's home nation.
Ahead the match, the duke joined Japan’s Crown Prince Akishino in the stands for the Rugby World Cup final in Yokohama after predicting it would be a "fantastic game".
Harry arrived in Tokyo on Saturday, with wife Meghan and son Archie remaining at home, and delivered a good luck message to the England team from the Queen.
Before the match, the duke said the tournament had been "incredible", and praised Japan for its hosting.
Earlier, Harry warmed up for the final at a training session for would-be Japanese Paralympians - and discovered that one or two of them were rooting for England’s opponents.
"Who are you guys supporting tonight?", he asked a group of wheelchair rugby players at Tokyo’s new Para Arena for disabled athletes.
Back came a chorus of "England" before Tomoshige Kabetani piped up: "South Africa!"
"I’ll have a word later," joked Harry. "You might not get selected for the Paralympics!"
Tomoshige, 32, explained that South Africa had been Japan’s last opponents in the tournament, hence his support for the Springboks, before adding: “This year you became a father. We are so happy.”
At which point the whole group gave the duke a round of applause.
Harry was shown around by power-lifter Eri Yamamoto, 36, who hopes to compete at next summer’s Tokyo Paralympics.
Having been at the 2012 London Paralympics as part of the Japanese support team, she told Harry that she hopes that Tokyo 2020 can be a worthy successor.
"London set the bar very high," she said.
The duke explained how 2012 had transformed public interest in disabled sport - "it’s just got bigger and bigger," he said - and he wished Tokyo well for next year.
Harry also met a group of schoolchildren including Shiyo Sudo, 12, who said that he was "very handsome" and pointed at his wedding ring.
"I’m married!" Harry said proudly, holding up his left hand to cheers and hoots of laughter.