The Cobblers reached the second round of the FA Cup after a five goal thriller at Sixfields. But it came at a cost.
With resources stretched to the limit, Kevan Broadhurst's men could scarcely afford another bad injury. But defender Paul Rickers was stretchered off in the first half after suffering a broken leg following a challenge from the visitors' Tom Bennett.
Broadhurst said: " It is difficult to form an oppinion from ground level but the players were incensed and Paul has said himself that he feels the player came in high and late." Northampton looked to be cruising at half time as they led 2-0 with goals from Paul Harsley and Marco Gabbiadini.
Harsley opened the scoring in the ninth minute with a 30-yard free-kick which was deflected past Paul Bastock in the visitors goal. It was his first goal for the club after moving on from Halifax in the summer - ironically the club Boston replaced in the Nationwide League.
Gabbiadini struck his 10th of the season in the 35th minute when he arched his body to head in a left-wing cross from Chris Carruthers.
Boston's only decent chance of the first half was a left-foot volley be Mark Angel whick looped dengerously just wide, but the The Pilgrims stepped up a gear after the restart.
They had already gone close twice before Tony Battersby made it 2-1 from the penalty spot after substitute Richard Hope was adjudged to have brought down Lee Thompson.
Northampton restored their two goal advantage with 22 minutes left when Derek Asamoah fired past Bastock after great approach play by Gabbiadini.
Yet there was a sting in the tail when Alex Higgins headed in a Thomas Bennet free-kick with seven minutes left