The government has argued that the changes are a women's rights issue, while opponents have said they are indicative of the Islamization of Turkish society.
The final vote on the constitutional reform package received 411 "yes" votes in the 550-seat parliament. The two proposed amendments needed a two-thirds majority, or 367 votes, to pass.
The package amends the constitution to read that everyone has the right to equal treatment from state institutions such as universities and that no one can be barred from education for reasons not clearly laid down by law.
Turkey's ruling Justice and Development Party (AKP) submitted the amendments under a deal with the opposition National Movement Party (MHP). The proposals were passed in an initial parliamentary vote on February 6.
The Islamic-rooted government of Prime Minister Recep Tayyip Erdogan must now prepare legislation to change parts of the law on higher education for the ban to be lifted.
But the main opposition party, the Republican People's Party (CHP), has vowed to go to the Constitutional Court in an attempt to block the changes.
In a final appeal today, CHP parliamentary group Chairman Kemal Anadol urged lawmakers to avoid a move that will "lead to chaos in society."
Tens of thousands of people gathered in central Ankara to voice their opposition to the reform.
"They [the government] are playing an evil game with Turkey," said Abdullah Gulen, who attended the protests. "That is why we gathered here to stop this evil game. We all, as enlightened people, want to stop this evil game."
A similar demonstration a week ago in the capital drew tens of thousands of people at the mausoleum of Mustafa Kemal Ataturk, the founder of the Turkish republic who entrenched secularism.
The government argues the ban means many girls are denied an education, and points to public-opinion polls that show that two-thirds of Turks support lifting the ban as evidence that the moves are democratic.
Establishment groups such as the judiciary, business organizations, and academics have all condemned the plan to lift the restrictions, saying this is a first step to allowing Islam to figure more prominently in public life. The military has refused to get involved in the debate but has made it clear they are watching events carefully.
To allay concerns, and as part of the compromise deal with the nationalists, the legislation places limits on the freedom to wear a head scarf at universities. The ban will remain in other areas of public life, including civil service.
And the changes allow only the traditional head covering, which is more or less loosely knotted under the chin, while excluding the wrap-around version.
A strict head-scarf ban has been in force in Turkish universities since the late 1990s. But the situation has become increasingly ambiguous with some rectors declining to enforce the ban.