They are angry at what they say is the curtailment of Islamic law.
The changes must still be approved by the Pakistani senate in order to take effect.
Under the Protection of Women Bill, judges will now have the discretion to try rape cases in a criminal rather than an Islamic court.
Until now, rape victims had to produce four – usually male - witnesses to the rape in order to result in a conviction. If not, they could themselves be prosecuted for adultery.
The laws formed part of the Hudood Ordinances introduced in 1979 by Pakistan’s then military ruler, Zia-ul-Haq.
"We are fully aware of the fact that we still have a lot more to do"
Pakistani prime minister
The changes, if approved, will allow convictions to be made on the basis of forensic and circumstantial evidence.
Shaukat Aziz, the Pakistani prime minister, said after the vote would "help lessen to a great extent the unfair and illegal treatment meted out to women".
But, he added, "we are fully aware of the fact that we still have a lot more to do."
Women’s rights groups meanwhile have given the vote a cautious welcome.
"We wanted a total repeal of the 1979 rape law, but the government has not done it," Hina Jillani, a leading Pakistani activist, told the Associated Press news agency.
Conservative opposition politicians have said they will fight to make sure the bill does not pass the senate stage.
"We reject it," said Malaun Fazlur Rahman, head of the Jamiat Ulema-i-Islam (Islamic Party of Religious Leaders).
He said the vote was a "dark day" for Pakistan.