Millwall 1 Scunthorpe United 2
All the action came in an enthralling second half with hard working Gary Alexander putting the hosts ahead with his clinical finish on 63 minutes before Hooper's brace took the Iron back up the M1 with a much needed victory.
There was little to choose between the sides, who started the afternoon level on points in fourth and fifth.
Kenny Jackett's Lions set off at a frantic pace, threatening a breakthrough four times in the first 15 minutes.
Goalscorer Alexander was the main aggressor as he forced fine saves from Joe Murphy with two goal-bound efforts.
Grant McCann fired the visitors' only serious chance of the half when his curling free-kick went inches wide towards the end of injury time.
With the game in the balance, Alexander broke the deadlock having raced into the clear on to Adam Bolder's defence-splitting pass and his clinical finish looked to tie up the win for the home side.
Just seven minutes later, Hooper was on hand to tap home Garry Thompson's crashing volley to level.
With both sides seeming to settle for a draw, Hooper popped up once again to secure the victory three minutes from time.
Having latched on to Matt Sparrow's pass, he buried past stranded David Forde to the visitors' delight.