O'Neill's management team, including former captain and Manchester United star Roy Keane, have also left their positions, FAI said in a statement, reports Efe news.
"The Board of the Football Association of Ireland has mutually agreed with Martin O'Neill to part company," FAI said.
O'Neill, 66, originally from Northern Ireland, was at the helm for five years, during which he took charge of 55 games, leading the team to the Round of 16 at the European Championships in 2016.
His tenure also featured wins over Germany, world champions at the time, and a run to the playoffs for the 2018 FIFA World Cup.
"There have been many highlights during Martin's reign - none more so than Euro 2016 in France, which will live long in the memory of all Irish supporters," FAI chief executive John Delaney said.
O'Neill departs after the team's recent poor performances in the newly-created UEFA Nations League, in which Ireland were relegated into group C after finishing at the bottom of their group which featured Denmark and Wales.
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