Khoi, 17, entered the competition as the top seed with an Elo rating of 2516, and scored 6.5 points with six wins and one draw from seven rounds.
In the eighth round on Sunday the 17-year-old Vietnamese International Master beat the Philippines' Jeth Morado (Elo 2219) in 36 moves to go to 7.5.
Despite not playing the ninth and final round yet, Khoi was named the winner since he was one point ahead of second-placed Indian IM K.S. Raghunandan (Elo 2441) and with a better head-to-head record against him.
Khoi's rating performance after the first eight rounds was at 2754, equivalent to that of a Super Grandmaster, and his performance has fetched him 15 Elo points.
By winning the event, he also won his fourth Grandmaster norm and is likely to be awarded the Grandmaster title during the evaluation period in September.
Earlier, he had also won the rapid chess event. He is expected to score a hat-trick by winning the blitz event to be played on Monday.
The 2019 Asian Junior (Open and Girls) Chess Championship is taking place in Solo, Indonesia, from July 1 to 8.
It has attracted 34 boys and 36 girls from Bangladesh, Hong Kong, Indonesia, India, Iran, Kazakhstan, Malaysia, New Zealand, the Philippines, Taiwan, and Vietnam.