The Italian, who oversaw a summer overhaul of the squad under which 14 players were brought in under former manager Paolo Di Canio, is set to leave with two weeks of the current transfer window still to run.
A club statement said: "Sunderland AFC has announced that the club has parted company with director of football Roberto De Fanti.
"The club would like to place on record its thanks to Roberto and wishes him well for the future."
De Fanti was drafted in along with chief scout Valentino Angeloni and an extensive network of scouts in June last year in a move designed to revolutionise the club's recruitment wing.
However, despite heavy investment, the Black Cats find themselves still fighting to stay in the Barclays Premier League with Di Canio's replacement, Gus Poyet, having rekindled their survival hopes in recent weeks.
It is understood that Short may not yet be ready to abandon the director of football post, but that there is currently no ready-made replacement waiting in the wings.
In the meantime, chief executive Margaret Byrne, who conducted the administrative side of transfers before De Fanti's arrival, will resume that responsibility with Argentinian defender Santiago Vergini having arrived in the north-east on Thursday with a view to tying up a move.
The last few months have proved difficult for owner and chairman Short, who opted for radical change after deciding his move to appoint Martin O'Neill as manager had not worked out as he had hoped.
O'Neill was shown the door at the Stadium of Light in March last year, but the Texas businessman took something of a gamble when he decided to replace him with fiery former Swindon boss Di Canio.
The Italian's arrival paid early dividends - victories over Newcastle and Everton paved the way for a successful survival fight and persuaded Short that his long-terms plans for the club could be fulfilled under the new regime.
As a result, he handed De Fanti the task of rebuilding the squad and the finance with which to do it with the focus on potential rather than expensive proven talent.
Unfortunately for the director of football, the results of his summer spree were mixed with the likes of keeper Vito Mannone and Italy international midfielder Emanuele Giaccherini having impressed, but many more - perhaps most notably £6.5million United States striker Jozy Altidore - having struggled to make a mark.
Di Canio departed just seven games into the new campaign having presided over a chaotic episode in the club's history which saw him criticise players publicly and famously address the fans directly on the pitch at West Brom after a 3-0 defeat, which proved to be his final game in charge.
He left in September with the club having collected just a single point, and Poyet has worked tirelessly during the months since to drag the club back to the brink of safety.
They head into Saturday's home clash with Southampton knowing victory could lift them out of the bottom three and pave the way for a climb up the table which looked unlikely during the latter days of Di Canio's reign.