Goalkeeper Rafi Mundiato became the match favourite blocking two attempts from the Vietnamese side after another kick from the visitors went wide.
The hosts also missed two chances in the penalty, but it was still enough for them to win the championships for the first time in the nation's history.
It was Mundiato's day as he successfully saved consecutive attacks from the Vietnamese side who won all matches in the lead up to the final.
At the 28 minute mark, Vietnam's Thanh Tung lodged a ball from the left wing in a straight shot which was diverted by Mundiato.
The star goalkeeper continued to frustrate Vietnamese players as he produced another strong defence from Cong Phuong's attempt 10 minutes later.
Indonesia has several chances to pass Vietnamese keeper Ly Van Truong however they failed to capitalise on opportunities during the 90-minute match and the 30 minutes of extra time.
The victory also helped Indonesia recover their 1-2 loss to Vietnam during a group round match on September 14.
In a separate match, Timor Leste overcame Laos 4-2 to take the bronze medal.
(Source: dangcongsan.vn)