Once the pupil, photographed as a boy alongside his childhood idol Phelps, he put in a masterful performance to deny the American a 23rd and final individual gold in a race that will also be long remembered for a three-way dead-heat for second.
Phelps, the defending champion and world record holder who is heading into retirement -- again -- after Rio, took silver along with two of his greatest rivals in a fitting finale before he bows out in Saturday's 4x100 medley.
With South Africa's Chad Le Clos the middle man, and Phelps and Hungary's Laszlo Cseh flanking him on either side, they joined hands and stepped up together to the podium.
"I'm just ecstatic. I don't think it has set in yet. It's just crazy," said Schooling, 21.
"It's been a hard road, I've done something that no one in our country has done before. I've received a lot of support and that's phenomenal."
Phelps, who now has 27 Olympic medals, had been hoping to win the event for the fourth successive Games but his Midas touch deserted him and he had to settle for another color medal for the first time in Rio.
His tally now reads 22 golds, three silvers and two bronzes with every chance of one more to come.
"I don't know if I've (ever) been in a tie, so a three way tie is pretty wild," said Phelps.
"It's kind of special, and a decent way to finish my last individual race. Can't complain too much," he said.
Le Clos, who lost his 200 butterfly title to Phelps on Tuesday, failed in his bid to turn the tables but was happy not to have been beaten by him again either.
"Strange is not the right word. Need to create a new one for that," he said. "I got silver tie in London so a three way tie is crazy. Maybe in Tokyo a four way tie."
The silver was the fourth of Cseh's Olympic career and left him, at 30, still without a gold.
At least year's world championships in Kazan, Russia, three women tied for 200 breaststroke bronze - Spain's Jessica Vall, Denmark's Rikke Moeller Pedersen and China's Shi Jinglin.
Two women's freestyle golds were handed out on Thursday after Canada's Penny Oleksiak and Simone Manuel of the United States recorded the same time.
The 1984 men's gymnastics saw four tied for silver in the vault.