Margate manager Chris Kinnear and assistant Kevin Raine have been suspended with immediate effect, reports BBC Radio Kent.
Kinnear was suspended after Tuesday's game
The decision was taken at a specially convened meeting held after Tuesday's 1-1 draw against Windsor & Eton in the Ryman League Premier Division.
Striker Danny Hockton scored the goal for Gate while captain Berti Brayley was sent off.
Margate are now seeking to appoint a caretaker manager.