The Cobblers kept up their play-off push with a seventh consecutive home league win - but the goals came from unexpected quarters.
All the pre-match hype surrounded debutante Eric Sabin. The striker was only picked up on loan from QPR on Friday, although he had spent the last month on loan at Boston.
Cobblers manager Colin Calderwood admitted Sabin was a touch embarrassed about performing against the players he had viewed as team-mates for the last week, but he almost made it a dream start at Sixfields only for his fourth minute shot to be saved by Paul Bastock.
Sabin's pace and directness continued to be a problem for Boston, but it was an injury to his strike-partner Magno Vieira which allowed Steve Morison the chance to come off the bench, and it was the rookie striker who made the breakthrough 18 minutes from time.
Morison's low shot from 20 yards swerved in front of Paul Bastock and the ball somehow went under his body and trickled over the line.
Four minutes from time, Boston's agony was complete when Lee Beevers chested a cross from Sabin back towards his own goalkeeper but Ian Sampson nipped in to convert a volley into the roof of the net.
Boston created few worthwhile chances - perhaps not surprising as they have scored only eight goals on their travels in the league this season.
They did go close eight minutes before the break when a header from Graeme Jones was cleared off the line by Luke Chambers but that apart the closest they came was a couple of long distance shots from David Noble.
Pilgrims manager Steve Evans said: "Two defensive errors have cost us the game. I didn't think Northampton caused us any problems. Considering the resources, Colin Calderwood has at his disposal here I was pleased with the way we performed." Calderwood said: "It would have been nice to get a breakthrough in the first half but we know from past experience that when we score early on we are sometimes up against it in the second half."