The Boeing 737-400 with 107 passengers on board was en route from the Albanian capital Tirana to Istanbul, when it was hijacked in Greek airspace.
The place was then forced to land in the Italian city of Brindisi by two Italian F-16 fighter jets.
Confusing reports
Istanbul Governor Muammer Guler said 28-year-old Hakan Ekinci seemed to have acted alone, apparently bluffing the pilot into believing that he had at least one accomplice on board.
Transport Minister Binali Yildirim earlier denied initial reports that Ekinci and a second Turk believed to have acted with him seized the plane to protest against the pope's planned visit to Turkey in November.
"The information concerning the pope was not confirmed. ... These persons are seeking political asylum and have said so to the (Italian) police," Mr Yildirim told NTV television.
Turkish media has reported the hijacker entered the cockpit about 20 minutes after the plane took off from Tirana, threatening the pilots with a parcel which he claimed contained a bomb.
He asked the pilots to divert the plane to Rome, but was told there was not enough fuel and the aircraft eventually landed at Brindisi.
The Istanbul governor said there was no indication of the hijacker having links with any terrorist organisation.
Earlier reports claimed two hijackers had taken control of the plane with a message for Pope Benedict XVI.
Wanted man
Turkish authorities said the alleged hijacker was being deported back to Turkey where he faced arrest.
Ekinci -- reportedly a Turkish convert to Christianity and a conscientious objector -- deserted in May while on leave from his garrison in Istanbul, fleeing to Albania where he made an unsuccessful bid for political asylum.
"We were going to arrest him at the airport and hand him over to the military authorities," said the Istanbul governor.
He confirmed that Ekinci had written in late August to the pope, seeking his help to avoid military service in Turkey.
Passengers unharmed
A traveller on board the plane told Turkish television by cell phone that the hijacker apologised to passengers before surrendering, two hours after the aircraft was forced to land in Brindisi.
"He is now apologizing to everyone and is waving to us," Ergun Ozkoseoglu told the NTV channel as other passengers could be heard breaking into applause in the background.
"The passengers were panic-stricken, they were worried, but everybody was fine," said another passenger Sadri Abazi.