The plane landed safely at Brindisi, Italy, and all 107 passengers and six crew left the plane after brief negotiations with the lone, unarmed hijacker, Italy's aviation authority ENAC said.
Hakan Ekinci stormed the cockpit shortly after the Turkish Airlines flight took off from Tirana bound for Istanbul, and told the crew he had three accomplices who would blow up the aeroplane unless he could deliver his message, the pilot said on Wednesday.
Mursel Gokalp, the aircraft's captain, told reporters in Istanbul: "While the chief stewardess entered the cockpit to ask if we needed anything, the terrorist entered by force. I tried to push him out, but he was a big man and I failed to stop him.
"He said his only aim was to give a message to the pope and then he would submit himself to the police. He said that if he failed to deliver his message, his three friends at the back of the plane would detonate the plastic bombs they had."
Forced to land
Passengers on the Turkish Airlines plane had originally said that two men had hijacked the plane.
No other hijackers were found
when passengers were let off
No other hijackers were found when Ekinci let the passengers off the plane in Brindisi and surrendered to local police.
"When things ended he shook my hand, said he was sorry," the captain said.
Turkish television reported that Ekinci had recently converted to Christianity and was a conscientious objector, going against their initial reports that the hijack was staged in protest over the pope's planned visit to Turkey.
Letter to the pope
It said he had sent a letter to the pope in late August asking for his help to avoid compulsory military service in Turkey. It quoted the letter as reading: "I am a Christian and I do not want to serve in a Muslim army."
Authorities said that Ekinci had travelled to Albania in May and requested asylum on the grounds that he was a deserter from the Turkish army and feared punishment if he returned.
Albania refused his request and he was being sent back on the Turkish Airlines flight.
Ekinci demanded the plane land in Italy, but the pilot told him there was not enough fuel to reach his specified destination. Italian authorities said he wanted to go to Rome.
The passengers were flown on to Istanbul on Wednesday morning.