Neil Doyle, co-owner of Shelbourne, said there were “no words to do justice” to Duff’s accomplishments at the club and his impact on the league as a whole.
“We look back with immense pride on his time here. As a club, we move forward with confidence, knowing that the foundations we have jointly built will underpin our continued success. Thank you, Damien, for everything.”
Duff’s exit from Tolka Park comes before Shelbourne travel to play Waterford on Monday.
Former Bolton and West Ham defender Joey O’Brien, who was Duff’s assistant, will take charge of the fixture.
Shelbourne have been drawn against Irish Premiership winners Linfield in the first round of Champions League qualifying, with the ties scheduled for 9 and 16 July.
Duff, who won 100 Republic of Ireland caps as a player, took over at Shelbourne in his first managerial role in 2021.
After finishing as runners-up in the FAI Cup in 2022, he helped Shelbourne to a first league title since 2006 last year after a dramatic final-day victory over Derry City.
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