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They took an early lead, when Martin Gritton beat three Iron players in the penalty area before beating Tommy Evans. He should have scored before his 14th minute opener, but saw his effort well saved by Evans.
Steve Torpey and Paul Hayes both went close for United, and Arjan Van Heusden in the visiting goal did well to stop a Hayes shot with his legs.
Wayne Graves, brought in on the right win in the absence of Matty Sparrow, might have put them level in the early stages of the second half but he was off target.
Graves was then controversially sent off in the 57th minute, after being shown a second yellow for an alleged dive in the area.
Iron manager Brian Laws was fuming at the decision by the referee, and by the time the final whistle had gone he went on to piss off Torquay gaffer Leroy Rosenior as well.
United were a goal down and the visitors had a numerical advantage, but the 81st minute substitution which saw on-loan forward Steve McLean replace Paul Hayes.
Five minutes after his introduction McLean took advantage of a slip by Van Heusden, who failed to take the ball under pressure from Torpey, to fire home his first goal in claret and blue.
Leroy Rosenior, in the visiting dugout, was incensed by the goal and after kicking a water bottle was ordered to watch the final minutes of the game from the stands.
And he won't have liked what he saw, as a 95th minute one-two between McLean and Peter Beagrie resulted in McLean laying the ball off to fellow substitute Alex Calvo-Garcia whose right-footed short flew into the top corner of the goal to send the crowd wild.
After the final whistle Gulls goalie Van Heusden continued his protest with the referee, and was also shown a red card for his troubles.
Scunthorpe hit back to draw level in the 86th minute when substitute Steve McLean whipped the ball in off the underside of the bar and in a dramatic finale Alex Calvo-Garcia smashed the ball home from 20 yards to grab the points.