Legislators approved the changes late on Wednesday for a second time, overturning Sezer's objection to an article that reduces punishments for running religion courses without required government authorisation.
Turkey's leaders have vowed to press forward with EU-oriented reforms, despite misgivings within the 25-nation bloc about bringing the relatively poor, predominantly Muslim nation into the fold when the EU is suffering a crisis of confidence about the future of European integration.
The new code, the first major overhaul of Turkey's criminal law in 79 years, went into effect on 1 June, and is aimed at advancing the country's bid to join the EU.
Sezer argued that the revision reducing the punishment for running religion courses violated the constitution, saying laws should "ensure that basic rights and freedoms are not misused in a way that could harm the secular republic".
The revision reduces punishment for those who establish and run the unauthorised courses from the maximum three years to a maximum one year in prison and allows courts to commute the prison sentence to a fine.
Course teachers are no longer punished and a reference to closing down the courses was removed.
Critics say the religion courses measure was aimed at appeasing conservative constituents of Prime Minister Recep Tayyip Erdogan's ruling Justice and Development Party, which has roots in the country's Islamic movement.
Amendments to Turkey's EU-
oriented code were approved
Parliament late on Wednesday also ignored another Sezer veto and approved a technical measure that requires Justice Ministry approval for individuals charged with committing a crime abroad to be tried in Turkey.
Sezer said that the ministry's approval might be applied unfairly and violated principles of equality in the country's constitution.
Sezer must now approve the legislation but can send it to the Constitutional Court for cancellation.
The new Turkish code increases the rights of women and children. It recognises rape in marriage and sexual harassment as crimes, and includes tougher measures against rape, paedophilia, human trafficking and torture.
But is has been fraught with problems.
Journalists say language in the code is vague, and the laws could make it easier for the authorities to crack down on journalists. They have also said the changes made by the government to improve the code did not go far enough.
Previous criticism of governing party proposals to criminalise adultery led the entire package to temporarily be retracted in September while lawmakers negotiated the amendments in time for the October release of a key EU report on Turkey's reform progress.
The proposal to criminalise adultery was dropped in the final package.