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.
Leading marksman Martin Paterson also went close for Scunthorpe with a shot that Rachubka just managed to turn around the post.
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.
The game turned against Scunthorpe in the 71st minute when Kelly Youga collected his second red card in successive games for his touchline challenge on Crainey.
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 Joe Murphy.