The protestors burnt effigies of Jammu Kashmir Chief Minister Omar Abdullah, who has ordered a judicial inquiry into the deaths.
Streets remained deserted, shops and businesses shut, as the strike crippled activity. Security personnel patrolled the roads, as movement was restricted in the city.
The strike called by the All Parties Hurriyat (Freedom) Conference, also closed schools, colleges and many government offices in Kashmir.
Residents alleged the two women, were abducted, raped and killed by security forces in Shopian, 60 km from Srinagar.
The authorities denied that the women had been drowned in a stream. A police statement said the post-mortem revealed no marks of violence.