Ninh Binh claimed the VND1 billion (US$48,000) cash prize and a berth in the Asian Football Confederation (AFC) Cup next year.
The hosts Da Nang pocketed VND500 million ($24,000) as runners-up.
"We played all out to win the match today. It's a significant win for us in the last game of the football tournament. I would attribute our victory to the players and our fans," said Ninh Binh coach Nguyen Van Sy.
Ninh Binh started the match with a powerful squad fronted by Nigerian Omoduemuke Peter, Ivory Coast's Sannogo Moussa and Brazilian-born Dinh Van Ta (original name Rodrigo Mota Farias), all of whom were granted Vietnamese citizenship.
Da Nang struggled to overcome the 1-1 deadlock with Argentinean striker Gaston Merlo, Huynh Quoc Anh and Nguyen Minh Phuong playing below expectations.
Phan Anh Tuan netted the first goal of the match in the 19th minute scoring an early lead for Ninh Binh in the first half.
Da Nang hit back with a strong offence, failing to poke holes in Ninh Binh's defence until Gaston Merlo evened the score for Da Nang in the final minute.
Ninh Binh continued with only 10 players after Le Quang Hung was sent off with two yellow cards in the 70th minute.
In the penalty shootout, Ninh Binh goalkeeper Manh Dung proved an unstoppable force, carrying the side to a National Cup win.
(Source: Vietnamnews)