"Following assessment on an injury sustained in training, Williamson will leave the England senior women's squad and return to Arsenal for her rehabilitation," the FA said in a statement.
Sarina Wiegman's squad will also be without the services of Manchester United forward Alessia Russo (23) and West Ham United defender Lucy Parker (23), who received her first England call-up last week.
Arsenal defender Lotte Wubben-Moy (23) and Manchester United forward Nikita Parris (28), both part of this year's European Championship winning squad, have been called up to replace Williamson and Parker, while no replacement has been named for Russo.
England will return to Wembley Stadium for the first time since lifting the European Championship when they face World champions USA in front of a sold-out crowd.