Erdogan had said he was unable to meet the pope due to his attendance at a Nato summit.
He will now meet Benedict on the pontiff's arrival at Ankara airport before leaving for Latvia, said a Vatican spokesman.
Benedict's trip to Turkey - which begins on Tuesday - will be one of the most delicate trips ever made by a pope.
The visit was intended to be a primarily Christian event centred around a meeting with the head of the Orthodox Christians, but it has been overshadowed by protests against his visit.
Hundreds of Turks have already demonstrated to show their anger over his comments on Islam and European opposition to Ankara's bid to join the EU.
Güncelleme Tarihi: 20 Eylül 2018, 18:16
Religion of peace
The pope angered many Muslims in September when he gave a lecture that was widely interpreted as portraying Islam as a religion tainted by violence.
In response, thousands of Muslims around the world held protests and demanded an apology from him.
In the wake of the protests, a Christian priest was shot dead in Turkey and several churches were attacked in the Palestinian territories.
An Italian nun was also shot dead in Somalia by two men who wanted to protest against the pope's remarks. A Christian priest was beheaded in Mosul in Iraq by men who also demanded an apology from Pope Benedict.
Benedict later expressed regret over the pain his remarks caused, but stopped short of a full apology.
Turks hope for apology
Many Turks hope that the pope will use his visit to Turkey to apologise for his September speech.
Ali Bardakoglu, who heads Ankara's Directorate General for Religious Affairs, which controls Turkish imams and writes their sermons, said: "I think the attitude the Pope should take is that neither Islam nor Christianity is a source of violence."
One possible gesture of reconciliation will come on Thursday, when the pope will make a visit to Istanbul's Blue Mosque.
He already plans to visit the nearby Hagia Sofia, a Byzantine building that was one of the world's greatest churches before being converted to a mosque following the city's conquest by a Muslim army in 1453.
Before his 2005 election as Pope, the then Cardinal Joseph Ratzinger expressed serious reservations about Turkey's bid to be a member of the European Union, citing religious and cultural differences.
The Vatican now says it is not opposed to EU membership for Turkey and the pope has shied away from the topic since his election but the issue is expected be discussed during the visit.
Patriarch Bartholomew, head of the world's Orthodox Christians, has said he would tell the pope that the EU must not be a "Christian club" and that Turkey must be allowed to join.
Turkey began its EU entry talks last year but is not expected to join the bloc for some time.