The 15-year-old from Toronto landed two triple Axels to score 144.19 points for his clean long program — a season's best by almost eight points.
"That was the best free skate I have ever had," Nguyen said. "It was the first time I've ever done two triple Axels in one program and I hope to continue to do that."
Nguyen led after the short program, and then skating to Bach's "Air on a G String" and Fantasia and Fugue" in the free program, Nguyen produced a triple Axel-double toe, then his second triple Axel, before reeling off six more triple jumps.
"I took it as a new day. I didn't really think about what had happened in (Thursday's short program). I just told myself to take one element at a time," Nguyen said. "Just before I went into my starting position I told myself just to have fun. This was my third junior worlds so I really didn't have anything to lose. I enjoyed it very much."
The Canadian scored 217.06 points overall. Russia's Adian Pitkeev surged from seventh after the short program to claim the silver with 212.51 points. American Nathan Chen rose from sixth after the short to capture the bronze (212.03).
Nguyen is coached by Canada's two-time Olympic silver medallist Brian Orser, who also works with Olympic champion Yuzuru Hanyu of Japan.
"This was a good event with good skating, and Nam really skated for it to win this championship," Orser said.
Nguyen won't get much of a breather after his gold-medal performance as he's a member of Canada's squad for the world senior championships that begin March 24 in Tokyo.
"I have to get back to training on Tuesday and I leave for worlds on Saturday, so I just have to enjoy the moment as much as possible now and when I get back I focus only on the senior world championships," Nguyen said.
When Nguyen was assigned to the senior world team, Orser cautioned his young skater "not to get ahead of himself."
"I said we have to get through junior worlds and do a great job there, and then we would shift gears after that for worlds. He was really able to do that and I was proud of him for that," Orser said. "He is really on such a great emotional high to carry him through, so he is just going to ride this wave. He has had a really busy season with 12 or 13 competitions, and he has just gotten better and better at each one."
Canada's three-time defending world champion Patrick Chan, who won silver at the Olympics last month, won't compete at the world championships.