United found an equaliser through Michael Collins, and two quick-fire injury time strikes from Mark Duffy (penalty) and Karl Hawley.
Despite the effort on the day, Colchester's victory away at Carlisle meant that the Iron were relegated to League Two to end a disappointing season.
The Iron started the the final game of the season at a busy Glanford Park knowing they must win to stand a chance of avoiding relegation from League One. Just one change had been made from the victory at Stadium:MK last weekend, with Christian Ribeiro being replaced by Eddie Nolan who has recovered from a knock.
Sam Slocombe continues in goal with a defence of Eddie Nolan, David Mirfin, Paul Reid and Tom Newey.
The midfield consisted of Mark Duffy, Michael Collins, Jimmy Ryan and Anthony Forde with Matt Godden and Karl Hawley completing the starting lineup up front.
The Scunthorpe bench was made up of James Severn, Christian Ribeiro, Mike Grella, Robbie Gibbons, Callum Howe, James Alabi, and Hakeeb Adelakun.
The game started brightly for the Iron with Godden breaking down the right from a Hawley layoff to win a corner inside the first minute. Godden twisted and turned again to win a second. Hawley, Godden and Forde caused most of the issues early on for the Robins down the right flank.
In the 12th minute, Swindon managed their first real attack, with a James Collins cross to the back post taken with relative ease by Slocombe. Collins broke again in the 17th minute after a good pass from midfield but Mirfin was able to hold him off in a foot race for Slocombe to collect.
A corner in the 22nd minute broke to the edge of the box where Jimmy Ryan was waiting. His fierce drive was blocked inside the 'D' before Reid hit the rebound over the bar from distance. A minute later another long distance effort, this time from Michael Collins, ended up in the AMS stand.
Swindon looked threatening on the break with the pace of Gary Roberts and Massimo Luongo carrying Town through the Scunthorpe midfield. He laid a ball off to Collins, who again found himself in space to shoot low to Slocombe's right who managed to smother the ball.
In the 30th minute, after a decent passing move Swindon played the ball deep towards the back post, where Gary Roberts headed past Slocombe, only to be flagged offside. Adam Rooney broke a minute later, one against one with Reid. The Robins striker jinked before shooting low. Slocombe was called into action again with a strong hand low down to his right.
Slocombe was busy again in the 34th minute with a good take from a Roberts free-kick thirty yards from goal.
On 35 minutes Town's good spell lead to a header from Joe Devera which hit the outside of the upright with Slocombe stranded. In the same attack, James Collins again tested the Iron keeper, who proved up to the test, saving low to his right.
In the 38th minute, Slocombe again saved, this time at his near post from a De Vita effort to hold off Swindon who had a strong ten minutes leading up to half time.
Scunthorpe managed to wrestle their way back into a spell of possession towards the end of the first half, putting an end to Swindon's good spell.
The first action of the second half came on 47 minutes with a Swindon corner. Slocombe committed and missed the ball but the Robins were unable to poke the ball home from a tight angle.
Up the other end, in the 49th minute, Scunthorpe earned a corner after a good break - with Hawley forcing a save from Foderingham. From the corner, the Iron again tested Foderingham who punched clear after a glancing header from Matt Godden.
In the 57th minute, good work from Scunthorpe's right back fed Mark Duffy on the left flank. His mazing run took him past a couple of Swindon players before he drove narrowly wide of Foderingham's right post.
Brian Laws made two changed in the 60th minute, with Christian Riberio and James Alabi coming on for Jimmy Ryan and Matt Godden respectively.
Slocombe's busy afternoon continued as he palmed James Collins' low cross away from danger on 62 minutes with a Swindon man lurking.
Scunthorpe earned a free-kick on 67 minutes through a tug on Alabi. Duffy's effort was spilled by Foderingham down to his left but the Swindon keeper managed to recover quickly to hold the ball.
Hakeeb Adelakun replaced Anthony Forde on 73 minutes for the Iron with the little happening for either side in the game. A minute later Kevin MacDonald freshened his side up with two changes - De Vita and Rooney leaving the pitch with Miller and Williams their replacements.
On 78 minutes Gary Roberts fired into an Iron defender from the edge of the box after good play down the right from Swindon.
In the 80th minute, Michael Collins was set free after getting infront of Devara, but the Swindon centre back managed to recover and put the ball out for a corner. Up at the other end, the Iron skipper Paul Reid made a good sliding tackle in the box to block an effort from Swindon's James Collins.
In the 82nd minute it was James Collins who broke the deadlock for Swindon, sliding in to convert a low cross from Andy Williams.
Following Swindon's opener, Scunthorpe rallied and after a good spell of pressure, Michael Collins poked home from a corner after the ball came loose inside the box to give the Iron faithful some hope going into the final few minutes.
In injury time Alabi earned a penalty after Foderingham rushed out and brought him down on the left side of the box. Duffy stepped up and slotted calmly into the bottom left corner to give Scunthorpe the lead.
Deep into injury time, Ribeiro made good progress down the right flank and managed to get a low cross into the near post. Hawley flicked the ball past Foderingham from inside the six yard box to make it 3-1.