Members of pro-Palestinian group Boycotts, Divestment and Sanctions (BDS) are campaigning against the singer's partnership with major South African retail group Woolworths, over its imports from Israel.
The South African branch of the BDS movement vowed to hold "the largest protest any artist would have faced since the end of apartheid" at Pharrell's concert at Cape Town's Grand West Casino.
On Friday the group won a court battle against an attempt by Cape Town authorities to limit the number of demonstrators to 150, and said it expected 40,000 people to turn out.