Success at York Street put Colin Calderwood's side right back in the hunt for a place in the top seven, particularly with games still in hand on most of the teams around them.
But the results left Boston further detached in mid-table as their previously impressive home record was dented again.
There was little to choose between the sides in the opening exchanges on a quagmire of a pitch.
Best early moments for the visitors were shots from distance by David Rowson and Danny Crow which brought Nathan Abbey into saving action while at the other end a 15-yard angled drive by Andy Kirk was parried away by Lee Harper.
Boston went close again on 20 minutes when Paul Ellender got on the end of a David Noble cross, but Harper was well positioned to save his header.
In the 25th minute, Northampton broke swiftly and Martin Smith cut in from the left only to see a rising drive flash inches wide.
Eleven minutes before the break, Boston threatened again and a fierce shot from outside the area by Noble was deflected wide.
Boston carved out a great chance after 44 minutes when Danny Thomas crossed from the left for Steven Boyack to force an excellent save from Harper before Jason Lee fired the rebound wide.
Boston had the better of the second half's initial creativity but without finding a way to trouble Harper.
The visitors, though, went closest to breaking the deadlock on 62 minutes when a rising 18-yard shot from Lee Williamson was tipped over by Abbey.
Northampton kept up their attacking impetus and in the 70th minute a swerving shot from distance by Rowson flashed wide of a post.
But three minutes later the visitors went ahead. Smith cut inside from the left, beat two defenders and drilled low across the face of goal - the ball appearing to deflect in off a home player.
Eight minutes from time, the visitors went close again when Crow found space to shoot but his low effort from 18 yards was held by Abbey.