Le Van Son opened the score with a spot kick at the 15th minute while maestro Nguyen Cong Phuong added two goals in the second half to give the host the convincing victory, the trophy and the US$12,000 cash prize.
Thailand won the US$7,000 prize for second place. Viet Nam's U21 team fought back to win over Malaysia's U21 team, 2-1, to finish third in an earlier match yesterday.
Hoang Anh Gia Lai, the host U19 team, finished their seven-year course at the Arsenal style football academy and used a one-way play for most of the first half.
Thailand set up a crowd defence to block stormy attacks from the host with home support going crazy. Xuan Truong made the crowd roar just 11 minutes into the game with a long-range shot, which went high over the bar.
In the 16th minute, Nguyen Cong Phuong, the winning team's captain, earned a penalty kick when he was pulled down in the 18-yard box after breaking through Thailand's defence. Le Van Son then scored on the penalty kick.
Four minutes later, Nguyen Van Toan missed a clear chance to score his goal when he made a solo at the left corner, but his shot went wide off the post.
Thailand launched a lone attack in the first half as they played a small line-up to limit the power of Gia Lai and reserve energy for the second half.
Gia Lai kept pressing the visitors in the second half, but Thanh Tung and Hong Duy failed to take advantage of clear opportunities.
Thailand ramped up its play with an attack in the second half. At the 56th minute, substitute Boonkerd Chaiyasin fired a shot while on a rapid attack, but Vietnamese goalkeeper Pham Van Tien saved the ball.
At the 76th minute, maestro Cong Phuong teamed up with Thanh Tung in the penalty area before firing an accurate shot to the back of the net.
Nguyen Van Toan missed two clear chances at the 88th and 91st minutes when his close-range shots failed to hit the target.
Thailand's players nearly lost control of the game and pushed the squad forward to pull back a goal.
At the 5th minute of injury time, Cong Phuong found his second goal of the game when he tapped the ball in from Thanh Tung's cross following perfect teamwork.