The Italian guided the Robins back into League One as fourth-tier champions at the first time of asking, and in his first season as a football manager.
Town interim chairman Jeremy Wray told the Swindon Advertiser: "This season he's done a great job but he's only halfway through. I fully expect him to pick up another trophy next year."
Di Canio beat fellow nominees Martin Ling of Torquay, Mark Yates of Cheltenham and Graham Turner of Shrewsbury to land the award, which was presented at Old Billingsgate in London on Monday night.
Wray added: "It's a thoroughly deserved and proper recognition of what he has achieved in his first season in management.
"He's been honoured by his fellow professionals and he fully deserved it. He's done a fantastic job and seeing everyone stand and applaud him says it all."