The match was briefly halted after Williams drew attention to alleged racist sounds coming from the Estadio Civitas Metropolitano crowd.
Things have gone off the boil for Ten Hag at Old Trafford.
Chelsea thought they had overturned a 2-0 half-time deficit when Axel Disasi headed home, only for it to be ruled out for a foul on Diego Carlos.
Harry Kane scored twice for Bayern Munich.