The deal also calls for the release of 200 Syrians jailed by President Bashar al-Assad's regime, according to sources close to the Turkish and Qatari mediation which led to the deal.
The releases in Beirut came a day after the Lebanese Shiites abducted by rebels in Syria 17 months ago were transferred to Turkey and handed to Lebanese officials in Istanbul.
"The two pilots have been released and are now in the hands of the Lebanese General Security Service in Beirut," NNA said.
Pilot Murat Akpinar and co-pilot Murat Agca were abducted on August 9 by a group which demanded Turkey use its influence with Syrian rebels to secure the release of the nine Lebanese.
Relatives of the Lebanese have repeatedly denied involvement in the kidnapping of the pilots, seized just outside Beirut's international airport, in an area controlled by Hezbollah, whose chief Hassan Nasrallah has denied any involvement.
Lebanese officials later said the Turkish pilots and the nine Lebanese pilgrims had boarded flights and were headed home. It was not immediately clear if the 200 Syrians had also been released.
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The Shiite pilgrims were snatched as they headed home by road in May 2012 after visiting holy sites in Iran, with rebels charging they belonged to the Lebanese Shiite movement Hezbollah, which backs the Damascus regime.
General Abbas Ibrahim, who heads Lebanon's Security Agency, had travelled to Damascus Friday to discuss a deal to free the hostages in exchange for Syrian prisoners.
The release of Syrian prisoners was a key demand of the rebels who abducted the Lebanese.
Qatari Foreign Minister Khaled al-Attiyah told Al-Jazeera television that Doha had also mediated the release of the Lebanese.
Attiyah was in Turkey and would accompany the pilgrims back to Lebanon, where a delegation of Lebanese ministers was awaiting their return along with families of the hostages.
The abductions prompted Turkey to urge its citizens to leave the country, and raised new fears about the impact of Syria's conflict on neighbouring Lebanon.
About a week after the kidnapping, Lebanese authorities arrested three suspects, whose identities were not revealed, a judicial source told AFP at the time.