Joe Garner's 71st-minute spot-kick proved the difference between the two sides as the promotion-chasing Swans were made to pay the penalty for not taking their chances.
Garner was the man brought down by Alan Tate as Scunthorpe, boasting the joint-worst home record in the second tier prior to kick off, claimed three crucial points to put them within touching distance of safety.
The scalp of Swansea adds to that of promotion rivals Nottingham Forest, who were undone by the same scoreline at Glanford Park only a matter of weeks ago.
But it could and should so easily have been a different story as Swansea, on the back of four successive victories, wasted a host of opportunities, although Garner thundered a late effort off the crossbar and Lee Miller clipped a post for the home side.
Source: PA
Source: PA