The United full-back was part of a squad revolt against coach Raymond Domenech during the World Cup in 2010.
Once the dust had settled, Evra was handed a five-match suspension for his role in the strike action.
"I spoke with Patrice at the time of the World Cup in South Africa. He suffered a lot - unfairly, in my opinion," Ferguson told RMC Sport.
"He was the spokesman for the entire group. He only expressed his personal view. But he was punished."
The 30-year-old has since been recalled to the squad by new coach Laurent Blanc.