It was the home side's first defeat in seven games, coming after they were reduced to ten men in the 17th minute.
Central defender Steve Foster was red-carded for use of an elbow in an aerial challenge on Brighton striker Sam Williams.
Seven minutes later it was the Seagulls that swooped with the opening goal when midfield man Dean Cox met a right-wing cross from Andy Whing with a diving header past keeper Joe Murphy.
Scunthorpe were rocked but forced their way back on level terms in the 43rd minute when leading marksman Billy Sharp netted his tenth goal of the season.
He fired his shot past goalkeeper Wayne Henderson at the second attempt after Brighton centre-back Adam Hinshelwood had headed against his own post while trying to clear a left-wing cross from Ian Morris.
It was Brighton that again started the second half in positive fashion. Substitute Jake Robinson forced a good save from Murphy before the visitors regained the lead in the 52nd minute.
Whing was again the provider with a cross from the right, low to the near post, where Gary Hart swept his shot past Murphy from close range.
Alex Revell might have struck again for Brighton midway through the second half with a good run into the box and a shot that Murphy only saved at the second attempt.
Scunthorpe poured forward in the closing stages in search of an equaliser, but the visitors soaked up the pressure well.
Hinshelwood was a star man in the middle of the back four, in his first full 90-minute appearance after 11 months out through injury.
Guy Butters was equally impressive as the Brighton defence kept a firm grip on Scunthorpe's highly-rated twin strikers Sharp and Andy Keogh.
It was just reward for manager Dean Wilkins, who made four changes to his starting line-up as Brighton ended a dismal run which started in mid-September.