The Gender and Equal Opportunity Bill was thrown out on Tuesday after some lawmakers voiced their opposition.
Rights activists say the bill would promote women's equality in marriage, inheritance and education.
Those opposed to the Equality Bill say it is not compatible with Nigerian culture and religious beliefs.
Some MPs also argued that the constitution already recognises the rights of everyone.
In Islam, women get half of men's share in inheritance and it is unacceptable for anyone to change that, a Muslim senator told the BBC.
One Christian lawmaker also quoted some sections of the bible to condemn the bill.
But the decision has been widely condemned.
Human rights activist Bukky Shonibare says it was a sad day for Nigerian women.
"It shows how backward we are and how much we want to hold on to our lopsided religious and cultural beliefs," she told the BBC's Focus on Africa radio programme.
It is unfortunate that some men who see the emancipation of women as a threat are the ones being trusted with making laws and order, she added.
"Every Senator that voted against the bill should hide in shame," said prominent actress Uche Jombo.
Some activists have started circulating a petition urging the Senators to reconsider.
Nigeria's Senate has been condemned for rejecting a proposed bill aimed at eliminating "all forms of discrimination" against women.