The 16-year-old top seed was in fine form and remained unbeaten through the nine rounds.
He finished the tournament with a victory over fellow-Indian V Praneeth, an International Master, late on Friday.
Praggnanandhaa (Elo 2642) finished a full point ahead of second-placed IM Marsel Efroimski (Israel) and IM Jung Min Seo (Sweden).
Praneeth, with six points, was joint-third, but placed sixth due to an inferior tie-break score.
He will be part of the India B team in the open event of the 44th Chess Olympiad in Chennai next month.
Praggnanandhaa's coach R B Ramesh congratulated him after the triumph and said it will help boost his confidence.
"Congratulations to him for the victory. He was the top seed, so it is not a surprise that he won the tournament. He played well in general, drew three games with black pieces and won the remaining games. It will help boost his confidence," Ramesh said.