The Pilgrims had been good value for the fourth minute lead afforded to them by Jacob Hazel, but the match was turned upside down after the break.
Substitute Anthony Mancini levelled on 54 minutes and former United loanee Mani Dieseruvwe won it for Pools in the 61st minute.
United boss Ian Culverhouse had opted to name an unchanged XI ahead of kick-off - and the Pilgrims were rewarded within four minutes when HAZEL beat the offside trap to send an angled drive across Adam Smith and into the back of the net.
Pools had an opportunity to equalise when Dieseruvwe took the ball down in the centre of goal, but fired over the top from 12 yards.
Half chances fell to Hazel and Frankie Maguire before half-time - but the Pilgrims were unable to add to their early lead.
The match swung decisively at half-time, with Mancini introduced in place of Greg Sloggett. MANCINI drew Pools level within nine minutes of the restart after waltzing through some static United defending on the edge of the penalty area.
Cameron Gregory saved well to deny David Ferguson, but Pools were in front in the 61st minute when DIESERUVWE swivelled brilliantly to lift a rising effort beyond Gregory's outstretched right hand.
Hartlepool managed the game superbly, as both sides made a flurry of substitutions, and the closest United came to equalising was deep into stoppage time when Jai Rowe glanced Dan Mooney's corner narrowly wide.
Boston (4-3-3): Cameron Gregory; Jai Rowe, Michael Bostwick, Zak Mills, Cameron Green; Dylan Hill, Martin Woods (Pemi Aderoju 60), Frankie Maguire (Keaton Ward 80); Sam Osborne (Dan Mooney 71), Jacob Hazel, Tony Weston (Tom Leak 63). Subs (not used): Mitch Roberts, Adam Marriott, Ellis Craven (gk).
Hartlepool (4-3-3): Adam Smith; Kieron Freeman (Nicky Featherstone 72), Billy Sass-Davies, Tom Parkes, David Ferguson; Jack Hunter, Nathan Sheron, Greg Sloggett (Anthony Mancini 46); Roshaun Mathurin (Luke Charman 67), Mani Dieseruvwe (Gary Madine 80), Joe Grey. Subs (not used): Manny Onariase, Brad Young (gk).
Referee: Richie Watkins.
Attendance: 1,925 (144 visitors).
PIC: Russell Dossett.