The match had been in some doubt due to heavy rain in the South East, however the 250-odd Iron fans who had made the long jouney down found out at 2PM that the pitch was playable.
United should have opened the scoring half way through the first half when the referee controversially decided that Southend forward Tesfaye Bramble handled in the box.
Martin Carruthers hit the post with his last penalty kick against Bury, so Andy Dawson stepped up to take the kick.
However, from twelve yards out, his effort went horribly wide - the kind of shot that Justin Walker would have been embarassed of.
Shortly afterwards Torps saw a close-range effort blocked, but the Iron were made to pay for their misses six minutes before the interval when Leon Cort - younger brother of Newcastle United forward Carl - drove home a header from a corner to give the Shrimpers the lead.
Rob Newman’s side could have extended their lead after the restart, with Scunthorpe still coming to terms with their double misfortune.
Phil Whelan did force the ball into the back of the net 12 minutes into the half, but the assitant referee raised his flag to keep United in the game.
A 70th minute free-kick was the closest Southend United came to extending thier lead, Evans was left stranded when Damon Searle's quick free-kick came crashing back off the crossbar.
However the match was turned on it's head 17 minutes from time when the referee gave his second penalty kick of the match - again for an handball offence.
The ball was volleyed into Mark Jackson, where it struck him on the arm and United faced the prospect of going two goals down in a match where they had held there own throughout.
Kevin Maher, possibly with a subconcious sense of fair play, hit a weak shot which was kept out by Tommy Evans. The shot may not have been the greatest but it was still a great save.
There are certain moments that turn games, and that was one of them. Immediately Scunny counter-attacked and while the home fans were still holding their hands behind their heads Martin Carruthers had put the ball in the top corner past Darryl Flahavan from just inside the area.
Then with just nine minutes left United scored the winning goal of the game after a goalmouth scramble from a corner. Clifford Byrne headed the ball towards goal, but it was unclear whether Torps or Wayne Graves had got the final touch to force it over the line, early suggestions are that Torps got the final touch.
Maher had the final effort of the game with a 25 yard shot, but it was bread and butter stuff for Tommy Evans to hold.