The main secularist opposition party, the CHP, said it would appeal to the constitutional court to overturn the move.
Recep Tayyip Erdogan, Turkey's prime minister, said lifting the ban was essential for religious freedom in Turkey, a candidate for European Union membership.
In a statement, Gul's office sought to justify the amendments as an attempt to provide equal access for all citizens to higher education.
"The amendments do not conflict with the basic principles of the republic," it said.
It noted that legislators representing 80 per cent of Turkey's citizens had voted in favour of the constitutional amendments in parliament.
The government must still amend a law governing the state body for higher education before the changes can take effect.
The headscarf ban in universities dates back to the 1980s but was tightened in 1997 when army generals, with public support, overthrew a government.