Steve Clarke is hoping to keep Glenn Murray at Reading after his loan deal expired following the 2-1 win over Norwich.
QPR boss Harry Redknapp admitted he needs to strengthen his squad after his side's 0-0 draw with Crystal Palace.
The Magpies launched an investigation into an incident after the under-21 team's 2-0 defeat at Sunderland on Monday evening.
It was claimed the former Scotland international was involved in an altercation with 19-year-old defender Remie Streete.
A club statement confirming Donachie's resignation made no mention of any such incident and gave no reason for the 62-year-old's decision to leave his post. It said the club would be making no further comment.
Newcastle's loss in the second-string derby came two days after the senior team were beaten 3-0 at home in the Barclays Premier League by the Black Cats.
Donachie's resignation completes a turbulent week at St James' Park.
The Magpies sold their best player, Yohan Cabaye, without replacing him, before that match and earlier this week announced the departure of controversial director of football Joe Kinnear.
Alan Pardew's side are away to Chelsea on Saturday.