More than 15,000 fans filled Lach Tray Stadium and brought uncomfortable heat to visitors Binh Duong, who failed to find the outstanding performance they displayed during the V-League.
The confused defence gave Haiphong the opening goal at the seventh minute.
Ho Van Thuan made the entire stadium weep, clap and cheer as he broke into Binh Duong's area from the left wing and strongly ran to the net.
The goal awoke Binh Duong, but it was the day of Haiphong's goalie Nguyen ThanhThang, who blocked all of their attacks, including a threatening free kick by Le Tan Tai, a former teammate, in the first half.
Tai did not receive a warm welcome in his first return to the city, after saying goodbye months ago, and was replaced in the second half.
Coach Le Thuy Hai pushed his players to open more attacks, but forgot to ask them to protect their net.
Their defenders made mistakes and Andre Diego Fagan did not miss his chance, scoring the second goal from a close range.
They also allowed Binh Duong, who set a record with three V-League titles, to return home with another loss in the final of the National Cup. Binh Duong has never won this trophy.
Their managers had reason to restore a bonus of VND2 billion (US$95,000) hung up ahead of the game.
"I don't know how to explain my feeling now, I am very happy, and it is more than that," said striker Nguyen QuangHai.
"We have tried our best and received great support from our fans, thank you, to defeat the champions," he said.
Meanwhile, captain Nguyen Minh Chau said the trophy was a sweet gift for his team, who worked hard but did not have winning results at the V-League this season.
He wanted to send his thanks to coach Dylan Kerr, who lighted up the team's passion with football after a disappointing season and brought a competitive spirit to the team.