The Iron preserved their unbeaten away record after referee Matthew Scholes adjudged a 50-50 tussle between Ben Grist and Danny Whitehall should result in a spot-kick for the visitors - converted coolly by talisman Callum Roberts with 13 minutes to play.
The Pilgrims had led through Lenell John-Lewis' fourth National League goal of the season in the 55th minute.
Watched by the stadium's third highest crowd to date, including the largest away following so far, the Pilgrims served up a good performance against the Iron.
Rory Watson made a crucial 20th minute save to deny Kieren Donnelly, while Matty Carson crashed a 25-yard free-kick off target. Watson made another solid save to deny Marcel Lavinier.
United took the lead 10 minutes after the break when Donnelly latched on to Carson's quick throw-in. His shot was saved by Watson, with JOHN-LEWIS gleefully tucking home the rebound.
There was a huge chance to double the lead four minutes later, with John-Lewis and Carson putting the ball on a plate for Donnelly - but he was unable to stretch far enough to divert it past Watson.
John-Lewis then slammed wide of the near post following Donnelly's assist - before ROBERTS stepped up from the spot after Scholes awarded the Iron their spot-kick, after a few seconds' hesitation.
Boston (4-3-1-2): Rhys Lovett; Marcel Lavinier (Ben Grist 73), Connor Teale, Zak Mills (Tommy Fogarty 78), Alex Lankshear; Dylan Hill, Greg Sloggett, Matty Carson (Rocco Coyle 87); Liam Waldock; Lenell John-Lewis, Kieren Donnelly. Subs (not used): Michael Kelly, Jordy Hiwula, Manni Norkett, Bobby Jones (gk).
Scunthorpe (4-3-3): Rory Watson; Joe Starbuck, Jean Belehouan, Will Evans (Kian Scales 66), Branden Horton; Alfie Beestin, Joe Rowley, Oli Ewing; Callum Roberts, Danny Whitehall (Joey Dawson 78), Declan Howe (Carlton Ubaezuonu 66). Subs (not used): Dubem Eze, Max Brogan, Billy Chadwick, Zain Westbrooke.
Referee: Matthew Scholes.
Attendance: 2,866 (644 visitors).
PIC: Tim Hoff.