It was the Seasiders who started brightly without being able to create a clear-cut chance in front of goal.
Scunthorpe took command when centre-back Andy Butler fired them ahead in the 19th minute with his first goal of the season.
It was a powerful left-foot shot that goalkeeper Paul Rachubka did well to get a hand to but could not claw completely away before it crossed the line.
Butler was always a threat to the visitors from set-pieces and, just before the interval, went close to a second goal with a header that was cleared off the line by full-back Stephen Crainey.
Early in the second half Scunthorpe again went close to a second goal when young midfield man Jack Cork brought the best out of Rachubka with a delicate lob from 20 yards.
Both teams had penalty appeals turned down, Blackpool first when Wes Hoolahan went down in the box under a challenge from Matthew Sparrow, and then Scunthorpe when Cork appeared to be clipped as he tried to get in a cross.
Blackpool began to apply the pressure as they searched for an equaliser and defender Kaspars Gorkss went close with a header which flashed just wide of the far post.
Ten-man Scunthorpe looked to have held out for a precious three points until the 88th minute when substitute Keigan Parker got free in the box and squared the ball for fellow sub Flynn to side-foot an equaliser past goalkeeper Joe Murphy.