Saturday’s strike shut most shops, schools and offices in Srinagar and other major towns of the scenic Muslim-majority area and came after protesters on Friday torched a government vehicle and clashed with police.
The 25-year-old married woman from the southern district of Kulgam alleged she was abducted and raped by two armed men wearing Indian army uniforms on Tuesday.
Kashmiri separatists who called the one-day strike demanded an independent probe by human rights groups or the United Nations.
"It (the alleged rape) has once again exposed the real face of forces and substantiated that they are using rape as weapon of war here," said hardline separatist Syed Ali Geelani.
The Indian army said Friday it was taking the allegations seriously.
"If there is any truth to the allegations, then it is a criminal act and strict action must be taken," Kashmir valley army chief S.A. Hasnain told reporters in Srinagar, Indian Kashmir's main city.
But Hasnain also noted that "terrorists also wear military uniforms" in Kashmir, adding he did not rule out the possibility that rebels disguised as soldiers could have staged the attack to stir public anger against the army.
The region was hit by massive protests in 2009 over the alleged murder and rape of two women in Shopian district, next to Kulgam. Federal investigators later said the two had drowned in a stream and were never raped.
Wary of new unrest, police have set up a special team to investigate the latest incident while the army has also launched its own probe.
The protests were the first major demonstrations this summer and raised concerns that the region might see a return to the street violence which has rocked the state over the last three years, leaving scores dead.
A police statement said there were no "marks of violence or resistance" on the alleged rape victim's body.
State Chief Minister Omar Abdullah said a identity parade of soldiers would be held, adding that the "guilty won't be spared".
Kashmir is split between India and Pakistan, with the Indian-administered sector hit by a more than two-decade insurgency against New Delhi's rule that has left more than 47,000 people dead.