In an interview with Spanish journalists, Perez said his teammate Wolff would be "better off the in the kitchen" than on the race track.
His comments followed a test drive at Silverstone on Friday by Wolff that ended after one lap because of engine failure.
While some, including the female reporter who held the interview, felt the joke was a victim of context, many social media users accused the Mexican of sexism.
Though Wolff, who comes from Oban, later came to the defence of Perez, the Force India driver issued an apology. He said: "I recognise that my comment, even though it was intended as a joke, was absolutely out of place and also unacceptable.
"With Susie Wolff I hold a very close friendship and I admire her greatly for her determination."