France's Ntamack, who is set to play a prominent role for his country as they host this year's Rugby World Cup, crossed with less than two minutes left denying La Rochelle a domestic and Champions Cup double.
"What a last play," Toulouse head coach Ugo Mola told Canal+.
"He was pretty much dead on his legs out there, I thought about taking him off.
"He can make France world champions," he added.
Mola kept faith with his side from last Friday's semi-final win over Racing 92 for the repeat of the 2021 decider.
Mola's La Rochelle counterpart Ronan O'Gara named the same squad that won a second straight Champions Cup final in May.
Before kick-off, French president Emmanuel Macron was whistled as he was presented to the players on the pitch.
He is also expected to be present for the opening match of the World Cup at the same ground, when Les Bleus face New Zealand on September 8.
In front of a vocal sold-out Stade de France in warm early summer conditions, the score was 6-3 after a quarter of the game.
Ntamack mistakes
Toulouse's Thomas Ramos kicked two penalties and La Rochelle's Antoine Hastoy slotted one in temperatures reaching 28 degrees Celsius (80 degrees Fahrenheit).
After a tight first 25 minutes, Toulouse crossed as Argentina centre Santiago Chocobares pounced on Jonathan Danty's fumble in midfield to run in from 50m.
Ramos added the conversion to make it 13-3 before Hastoy cut the score to seven points with his second penalty on the half hour mark after his half-back partner Tawera Kerr-Barlow had chased down Ntamack near his own line.
La Rochelle ended the half the better and Kerr-Barlow burrowed over before Hastoy brought the scores level at 13-13 at the break.
O'Gara's side came out from the interval with intent and after a Pierre Bourgarit break France prop Uini Atonio powered over as Hastoy kicked the conversion to make it 20-13 with 35 minutes to play.
With 18 minutes remaining, Toulouse regained the lead as Ramos kicked three more penalties to make it 22-20 to set up a tense finish.
Hastoy responded with two efforts of his own for 26-22 with just nine minutes left.
A little over 60 seconds later Toulouse were handed a penalty and Ntamack's attempted kick to the corner went dead handing La Rochelle a scrum, instead of defending a lineout near their own line.
From that set-piece Toulouse were penalised and Hastoy cleared his lines as half of the Stade de France draped in yellow sensed victory.
Despite their hopes of maiden French crown their aspirations were dashed with less than two minutes on the clock thanks to Ntamack's moment of brilliance as he broke free from his own half to score to make up for his earlier errors.
Ramos then kicked the conversion with the Toulouse crowd delirious in celebration of their continued dominance of French rugby.
