Shane Byrne returned to haunt Brackley Town as Boston United booked their place in the FA Trophy draw.
The former Saints midfielder netted what turned out to be the winning goal on his first return to St James' Park since moving to Lincolnshire in the summer.
Danny Elliott put the Pilgrims in front on his return to the starting line-up before Byrne doubled the advantage, Lee Ndlovu's second-half finish setting up a tense conclusion as 10-man United clung on to make it three unbeaten.
Despite making a host of changes for the midweek Northants Hillier Cup victory against Daventry Town, Saints boss Kevin Wilkin reverted back to the starting XI which drew 0-0 with Curzon Ashton last weekend.
The Pilgrims were forced to make two changes from the starting XI which beat Darlington 2-0 on Tuesday, injured skipper Luke Shiels replaced by Scott Garner in defence while Jake Wright jnr - scorer of Boston's last three goals - was unavailable having been snowed in.
Leading scorer Elliott returned to the starting line-up and made his mark by opening the scoring in the 27th minute with an angled lob that Danny Lewis couldn't claw away.
Prior to that, James Armson had tested Pilgrims keeper Marcus Dewhurst with Elliott drilling wide at the other end.
Elliott struck the Saints' side netting before Boston doubled their advantage in first-half stoppage time.
Jordan Burrow won a loose ball and teed up his teammate who found the net at his old stamping ground from 20 yards out.
Having scored four times for Brackley against Boston Byrne, who won this competition with the Saints in 2018, saw his role reversed.
Boston had made the most of their first half wind advantage, with the Saints capitalising as the rivals switched sides.
Three minutes into the second half and Ndlovu pulled Brackley back into the contest, finishing from close range.
Dewhurst kept his side ahead as he denied Ndlovu a second, the Saints striker then flashing an effort wide.
Boston were down to 10 men ion the 84th minute as Scott Duxbury picked up his second yellow card of the game.
Having been shown the first red of his career three weeks earlier at Chester, he collected his second in as many away performances.
Town began piling the pressure on and Tre Mitford saw a glancing header fizz wide of the target.
Armson saw an effort smash the Boston crossbar before Dewhurst was equal to another effort.
SAINTS: Lewis, Myles (Yusuf 73), Franklin (Mitford 79), Murombedzi, Lomas, Dean, Lowe, Armson, Ndlovu, York, Walker; Subs (not used): Rolt, Cullinane-Liburd, Putz, Worby.
PILGRIMS: Dewhurst, Tootle, Duxbury, Platt, Garner, Green (Gordon 88), Burrow, Ferguson, Elliott (J. Preston 79), Ayina, Byrne; Subs (not used): Shiels, F. Preston, Leesley, Crook.