The coach was suspended on
Thursday afternoon for allegedly striking one of the club's Under-21 players.
However, the 62-year-old has now left the club, with a statement on the Magpies' official website confirming Donachie's exit.
"Newcastle United can confirm that Willie Donachie has resigned from his position as reserve team manager with immediate effect," the statement read.
"The club will be making no further comment."