The Italian had reportedly been considering his future after the club had sold Matt Ritchie to Bournemouth.
In a statement released to the Swindon Advertiser, Di Canio said: "Last Tuesday, 12th February, I formally confirmed my resignation as manager of Swindon Town Football Club with immediate effect.
"In my previous press statement on 1st February, I said that I was considering my future, as my position with the club had become untenable, after I found out that Matt Ritchie had been sold without my consent.
"Despite these problems, I have delivered everything and more that was asked of me, by achieving promotion last year as Champions and competing this season for promotion to the Championship and being just 3 points from top place a year earlier than expected."
Di Canio leaves Swindon with the club currently sixth in League One.