Substitute John O'Flynn grabbed the stoppage-time winner after Jacob Blyth gave the Cobblers the first-half lead only for Scot Bennet to equalise before the break.
Northampton's home form last season was the backbone of their play-off push but this time around they are struggling to reproduce their best at Sixfields, where the Grecians maintained their good start to the campaign.
"My players are devastated in the dressing room," said Boothroyd.
"We had five or six more opportunities than Exeter but you have to put those chances away and we didn't.
"(Northampton goalkeeper) Matt Duke has touched the ball twice, to pick the ball out of the net on both occasions. We've been done in the end by a goal which we shouldn't have conceded.
"It was a game we expected to win, certainly one not to lose, but that's football. I'm trying to focus on the performance.
"I'm pleased with a lot of things. The players did what I wanted them to do tactically, I asked for crosses and shots and I got all those.
"But football is like that sometimes. You can be rubbish and win and be brilliant and lose. It doesn't matter what we're doing at the moment, we're just not getting our rewards.
"It's not a nice feeling but we're not far away from where we want to be. It's all about the long haul and I have to remain focussed on that.
"Exeter are doing well and they're up at the top because things are going their way at the moment. We're down near the bottom because things aren't going our way but we've got to keep going, we'll play a lot worse than that and win."