The U's ended a run of three successive home defeats by striking twice in quick succession just before half-time through James Constable, in the 44th minute, and then Danny Rose's penalty, two minutes into stoppage time, after Constable was tripped by Ben Tozer.
The defeat keeps Northampton second from bottom in League Two.
Boothroyd said: "I thought we'd turned the corner after a good win last week, but five minutes of madness cost us here.
"We just knocked off when Constable scored.
"I don't think it was a penalty after that, but he shouldn't have got in there in the first place, and we were responsible for that."
Boothroyd said: "The effort is there, the willing is there. Unfortunately, the concentration for those five minutes wasn't there.
"But we'll come through it, we'll climb. The signs are there and the work ethic is there."
Northampton coach Tim Flowers, the former England goalkeeper, was sent from the touchline at half-time for what he said to the officials in protest at the penalty award.
"Oxford weathered the storm they got from us in the second half, and then looked to play on the counter-attack." Boothroyd added.
"Whereas Oxford had players coming back, we had more injuries. I didn't want to risk Hackett in case it put him out for longer."
- Sports & Recreation
- James Constable