Cameroon then thought they had pulled a goal back early in the second half, but VAR again ruled against them for a marginal offside - sparking more chaotic scenes.
Cameroon defender Augustine Ejangue also spat on the arm of England forward Toni Duggan.
The FIFA proceedings against the Cameroonian Football Association cover "alleged breaches related to article 52 (team misconduct) and article 57 (offensive behaviour and fair play) of the FIFA Disciplinary Code," world soccer's governing body said in a statement on Wednesday.
Cameroon coach Alain Djeumfa pointed the finger at the referee, calling the defeat a "miscarriage of justice".
England manager Phil Neville heavily criticised the behaviour of his side's opponents after the contest, which involved strong challenges throughout including one horrific tackle on England's Steph Houghton.
"I am completely and utterly ashamed of the opposition," the former Manchester United player said. "If that was my team - and it will never be any of my players - they would never play for England again."
(Reporting by Toby Davis; editing by John Stonestreet)
