Former Ipswich striker Richard Logan was the late hero for Boston United, with a winning goal three minutes into stoppage time.
Logan headed in from Tom Bennett's cross to spark scenes of jubilation which hoisted the Pilgrims out of the third division relegation spots, but leaving United's hopes of automatic promotion dented.
United controversially had Cliff Byrne sent off in the second half, and had seemed destined to prise a point from the encounter until Logan's header.
Boston opened strongly, but despite forcing five corners in the opening five minutes failed to create and clear goalscring chance.
Neil Redfearn saw a 20-yard free kick blocked, and in the 10th minute Simon Weatherstone fired their best chance off the underside of the bar following a cross from Logan.
Scunthorpe replied with a tame effort from Matt Sparrow before, back at the other end, Logan headed fractionally wide on 39 minutes from a Weatherstone cross.
Paul Bastock was the first keeper called into action after the break, smothering a downward header from Martin Carruthers following a cross from the left by Andy Dawson.
The game turned in the 57th minute when Scunny were reduced to ten men. Referee Andy D'Urso, who is on the Premiership list of professional referees, showed Cliff Byrne a straight red card after Mark Greaves went down under his challenge.
Despite the numerical advantage Boston still didn't look like to put the ball past Tommy Evans, with Logan's 68th minute header at the keeper.
Just when all seemed destined for a day of frustration for the home side, a 93rd minute slip by Alex Calvo-Garcia allowed Bennett to cross for Richard Logan to head home.