The B-Max Racing driver started second on the grid behind TOM'S man Hibiki Taira for the 19-lap contest, with Taira holding the lead at the start.
That was how the order remained at the head of the field until the start of lap 17, at which point Taira appear to suffer an issue and slowed, allowing Fraga and his pursuers, Enzo Trulli and Seita Nonaka, to close in.
Fraga swept past an ailing Taira on the back straight approaching Horseback corner, with Trulli and Nonaka also clearing their ailing TOM'S team-mate in the following turns.
From there, it was a straightforward run to victory for esports star Fraga, who restarted his real-life career this year by landing drives in both Super Formula Lights and SUPER GT's GT300 class.
"It's my first win for three years, so it feels quite good to be back on the top step of the podium!" Fraga told Motorsport.com. "It was a long two years with no racing, and three years without winning.
"But there's still a bit of myself that knows I need a bit more speed to be constantly in this position. I have to work hard with the team to make sure I have a good performance for the next round."
The battle for second was resolved in favour of Trulli when Nonaka spun at the first corner trying to attack the son of ex-Formula 1 racer Jarno.
It marks TOM'S driver Trulli's first podium in the series, after the rookie finished fifth and fourth in the first two races respectively.
Nonaka's spin allowed Shun Koide to take the final spot on the podium, with Nonaka recovering to finish fourth.
The first two races of the weekend had been won by Taira, with Fraga finishing second in the opener on Saturday and Iori Kimura proving Taira's nearest rival in Sunday morning's second race.
However, Kimura let a chance to gain points on Taira slip with a start-line infraction, which meant he was awarded a drive-through penalty that left him a distant eighth at the finish.
Super Formula Lights' other new international driver, David Vidales, had his weekend compromised by a first-lap clash with Yuga Furutani in the first race, for which Furutani was deemed culpable.
The Spanish driver scored a best finish at Sugo of fifth in the second race.
