Midfielder Nguyen Quang Hai pounced on a loose ball in the Viettel penalty area and volleyed home with just three minutes to go.
On 75 minutes, underdogs Viettel thought that they had sealed the win when midfielder Ngoc Son broke the deadlock in what up until that point, had been an uneventful affair.
But Vietel held their lead for just seven minutes. Ha Noi FC midfielder Truong Van Thai Quy made the most of confusion among the Viettel defence to power the ball home for the equaliser.
The goal sent shivers down the spines of the team in white who must have already thought their name was on the trophy.
But glory was not to be, and Viettel took their eyes off the prize and with three minutes to go, Hai was in the right place at the right time to slot home the winner with his trusty left foot.
Up until the final quarter of the game, the match had been a tepid affair.
On five minutes, Hai jinxed into the box from the left but his cross was too high for Nguyen Van Quyet.
The defending champions had all of the early exchanged, mainly from the guile of Hai who forced Viettel goalkeeper Tran Nguyen Manh into a good save on the ten minute mark.
Underdogs Viettel struggled to get a foothold on the game, but on 20 minutes, Nguyen Hoang Duc thought he had broken the deadlock but his effort crashed against the crossbar.
After the break, Viettel began to turn the screw and would be disappointed they never took the lead on 54 minutes from a corner but the strike was saved by Bui Tan Truong in Ha Noi’s goal.
Just before the hour mark, Bruno Cunha should have done better from the edge of the box but he dragged his shot wide.
As extra time loomed, Viettel broke the deadlock. But their hopes of lifting the trophy were dashed in a final ten frantic minutes at Hang Day Stadium.
This is the second time the team from the capital have lifted the National Cup, and the victory was even sweeter as it came against their capital rivals.
For the first time in 16 years, Ha Noi have regained the National Cup, a feat only achieved back in 2004 by Binh Dinh.
As for Viettel, that’s now four National Cup finals they have failed to win.