South Africa earlier qualified for the final by beating France 5-0 in the semi-finals of the event, played at Villaggio del Rugby in the Italian coastal city.
In the final, the Japanese team held a 5-0 lead at the break and extended that to 10-0 before Kurt-Lee Arendse scored in the corner.
Japan got their crucial third try with a minute to play and although Diedrick Oberholzer scored a try which he converted as well, the time was up on the clock and the Japanese could celebrate.
SA Students coach Pieter van den Berg was proud of the team’s efforts and said the fighting spirit of the side will be a lasting memory.
“The final result did not go our way and although that is disappointing, the way we kept ourselves in the match was very pleasing,” Van den Berg said.
“The margins between the sides were tight, but we showed tremendous guts and that helped us, especially against France, where we scored in the last play of the match to get into the final.”
Van den Berg congratulated Japan on their gold medal: “They scored the points when it mattered and edged us, so they deserve the gold. We are still immensely proud of our silver medal though. These players really showed a lot of commitment and pride to play for their country and the medal is good reward for that.”
• The SA Students Women's team missed out on a medal by the narrowest of margins. They were beaten 12-10 by Russia in the bronze final, so the team coached by Riaan van der Merwe finished fourth overall.
Scores were tied 5-5 at the break, but where the Russians converted their second half try, both South African efforts sailed wide.
Earlier in the day, they were beaten 19-12 by France, who scored a late intercept try in the semi-final, to deny South Africa a place in the final.