Cobblers boss Boothroyd, who took charge of the club in November 2011, guided them to a sixth-placed finish in his first full campaign.
The 42-year-old, who steered Watford to the top flight via a play-off final win over Leeds in 2006, said the team that finished four points ahead of Bradford did not do themselves justice in the showpiece.
Phil Parkinson's side stunned Bradford-born Boothroyd's Northampton with three goals inside the first 28 minutes from James Hanson, Rory McArdle and Nahki Wells to end a 64-game season on a glorious high.
"We looked like rabbits in the headlights for the first 30 minutes. Three-nil down is a massive uphill battle," Boothroyd said.
"What's most disappointing for me is that all I wanted was for that group of players to play to their potential on a fantastic stage and we didn't do that.
"When you come to a place like this you want to go away a winner. Bradford got what they deserved, so well done to them.
"We have to use this to our advantage. I've been a winner in a play-off final, 3-0, and now I've been a loser in a 3-0 final.
"But you've got to use it and not sulk, and bounce back quickly and that's what we'll do."