After an untidy first half by Rochdale the hosts improved after the break but they could not profit from the dismissal of Matt Sparrow after a midfield mini riot.
Martin Carruthers scored a couple of goals after 49 and 72 minutes and that looked like the end of the show for Rochdale.
But the home side began to show a bit of spirit in the last ten minutes.
Player-manager Paul Simpson pulled one back with a long-range shot five minutes from time.
With five minutes plus another four in stoppage time left Dale might have had enough time to do a repair job.
The chances were there but the takers were not although youngsters Paddy McCourt and Kevin Townson both made brave efforts to rescue a point.
Scunthorpe's defence was as good as Rochdale's shooting was bad and the chances were thrown away to give Scunthorpe their third away win in a row.
Iron boss Brian Laws said after the match: "It's not often that that happens to us but we're playing well and we deserved it."
Meanwhile Rochdale manager Paul Simpson said: "This is the worst week since I joined Rochdale. We practised things in training and then forget about them when we're in a match.
"We have some sorting out to do."
Rochdale lost last week at Hull and this second defeat does not help their promotion chances.
Against a ten-man side they should have created more chances but as it was only a good save from Matthew Gilks spared them a greater ignominy.
They were up against a side full of spirit and confidence but even so they should have done better than this especially against only ten men