Members voted unanimously to add gender to an anti-discrimination list that already includes religion, race, descent and place of birth.
Activists said the amendment would help change traditional attitudes and lead to more equality in the mainly Muslim nation.
Correspondents say the ruling party of Prime Minister Mahathir Mohammad has already been working to boost support among women, establishing a women's affairs ministry and appointing women to key government posts.
The change to article eight of the constitution was passed late on Wednesday by 127 MPs. There are another 21 MPs in the lower house but they did not attend.
"The time has come for gender to no longer be a factor for discrimination," said government minister Rais Yatim. "Be thankful to the government that this step has been taken."
Political appeal
Campaign groups welcomed the move.
"Women will be able to challenge decisions or procedures [in court] which discriminate against them on grounds of their sex," said Prema Devaraj, of the human rights group Aliran.
"This, of course, makes the amendment more than a symbolic act."
The ruling United Malays National Organisation party has been keen to boost support among women since it lost support in 1999 elections to the fundamentalist opposition Pan-Malaysian Islamic Party.
It has been playing on fears from some women that if an Islamic state were to be introduced, women would be made subordinate under religious laws.