Hooper, who netted a hat trick against the Seagulls earlier in the season, troubled them again all afternoon.
Scunthorpe dominated the opening half with Hooper and midfield man Matthew Sparrow both denied by the woodwork with headers that bounced off the crossbar.
Brighton looked like they might just hang on until half-time until Hooper finally struck with the opening goal after 42 minutes.
An excellent passing move opened up the visitors defence for Hooper to find the bottom corner of the net with an excellent finish for his 27th goal of the season.
Brighton pushed an extra man forward in the second half to try and get themselves back into the game.
They seldom threatened an equaliser though substitute Seb Carole should have done better just after coming on when he lifted his shot over at the far post.
Brighton were reduced to ten men in the 79th minute when centre back Matt Heath was red carded for bringing down Hooper in the box.
It enabled midfielder Grant McCann to make it 2-0 from the spot, crashing his effort past goalkeeper Mikkel Andersen who had earlier kept his side in the game with a string of fine saves.
While Scunthorpe remain in the top six, time is now running out for new Brighton Boss Russell Slade if he is to save the Seagulls from the drop.