Di Canio was installed as Black Cats boss in March but lasted just 13 games in the job despite guiding the club to Premier League safety last season.
He was replaced by former Brighton boss Gus Poyet, who Ellis believes can bring an end to the uncertainty at the Stadium of Light.
Writing in his programme notes ahead of Sunday's derby clash with Newcastle, Short said: "With the euphoria from our successful survival fight at the end of last season and the optimism surrounding our pre-season, we could never have imagined in our worst nightmare being in the position we are in now.
"The club has been in turmoil as a result of the change of head coach so early in the season.
"I have to take the blame for that. Clearly at least one of the decisions I made over the last several months was the wrong one.
"I believe this period of uncertainty is now over with the appointment of Gus Poyet.
"Gus' challenge at Sunderland is to establish stability, get what I consider to be a good squad of players together as a cohesive unit and to begin fighting or way back up the table.
"This will have to be a steady, one-game-at-a-time recovery."
Prior to Sunday's game, Sunderland have taken just one point from their first eight Premier League games, a run that leaves them bottom of the table.