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It was the first defeat in eight games for the home side who had plenty of possession in the early stages without being able to make it count.
But they finished the match a well-beaten side, as an in-form Blackpool, who played the last 20 minutes with only ten men following two yellow cards for winger Wes Hoolahan, secured the three points.
Blackpool snatched the lead against the run of play in the 27th minute when Andy Morrell squeezed home a shot at the near post from a cross by full-back Shaun Barker.
At the opposite end they kept a tight check on Scunthorpe's much-vaunted strike duo of Billy Sharp and Andy Keogh.
With Scunthorpe struggling in front of goal, it was Blackpool who struck again in the 58th minute when Hoolahan netted from the spot after Keigan Parker had been brought down in the box by goalkeeper Joe Murphy.
Hoolahan was booked for celebrating his goal and was then sent off in the 73rd minute after picking up a second yellow card for kicking the ball away at a free-kick.
But by then Scunthorpe were looking a well-beaten side and it was no real surprise when Parker waltzed through the middle of the home defence to make it 3-0 in the 88th minute as Blackpool stretched their run of form to just one defeat in the last 11 games.
Substitute Ian Baraclough salvaged a late consolation goal for the home side when he headed home a free-kick from Jim Goodwin.
But it was much too little, too late for Scunthorpe who suffered their first defeat since new manager Nigel Adkins took charge.