It came after former Glanford Park favourite Matt Sparrow had threatened to haunt his old club by firing the visitors in front early in the second half.
Sparrow, who spent over a decade at Scunthorpe, was making only his second appearance for the West Sussex team after joining them last month from Brighton.
Driving forward from midfield, he was left unmarked in the box to pick his spot in the 48th minute after good work down the right by Billy Clarke.
It was Crawley's first threat after struggling as an attacking force in the opening half which the Iron dominated.
But the home side could not find their finishing touch as Crawley goalkeeper Paul Jones pulled off three fine saves to deny Jimmy Ryan, Mark Duffy and Akpo Sodje.
It was the 67th minute before Scunthorpe got themselves back on level terms when midfield man Ryan smashed a shot home from close range after Jones had been able to only half-block an effort from Michael Collins.
After Jamie Proctor had rattled the crossbar for Crawley, it was Scunthorpe who then snatched a 78th-minute winner when centre-back Niall Canavan rose at the far post to head home a left-wing corner from Duffy.
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