The freed hostages left the bus from the driver's door shortly after midnight, and heavily armed police then searched the public bus. The two hijackers left the bus with their hands on the heads after throwing two shotguns out the door.
The hostage drama ended after hijackers had gradually released 17 of the 26 passengers during the day Wednesday. Relatives of the hostages, who were waiting in a nearby supermarket, ran up and hugged them.
Police said a preliminary investigation indicated the two men, both 24, were motivated by money and had planned to take the bus to Albania. At one point, one of the hijackers threatened to blow up the bus if authorities did not deliver a ransom of US$1.33 million by dawn Thursday.
They also told police they wanted to be taken to Athens airport and be flown to Russia.
"A preliminary investigation shows they wanted the money and their goal was to go to Albania. They said they wanted to go to airport to muddy the waters," Gen. Giorgos Angelakos, chief of the Greek police, told reporters.
He said the two men did not have any explosives and were only armed with shotguns.
"There were no explosives. The bag they had was empty. They said they had explosives to try and show us that they could do serious harm," Angelakos said.
The two men were identified as Gaz Resuli and Leonard Murati. Their hometowns in Albania were not available, but Angelakos said the had been living in Greece for the past six to seven years.
Giorgos Voulgarakis, the minister in charge of police, said the operation and negotiations to free the hostages "was one of the most difficult and complex incidents we have ever had to deal with."
He credited the success of the police with the training they received ahead of and during the Olympic Games. It was also the fifth time a bus has been hijacked since 1999.
"The experience we gathered during the Olympic Games did not go wasted," Voulgarakis said.
He also called on Greeks not to vent their anger on the hundreds of thousands of Albanian immigrants living in Greece.
The two men seized control of the intercity bus at 5:50 a.m. Wednesday at a bus stop in the Athens suburb of Geraka, about 10 miles east of the city center. The bus driver, a ticket inspector and a passenger escaped almost immediately.
Police praised the driver's quick action, which immobilized the bus and gave authorities control over the situation.
The hijackers initially demanded a new bus driver, saying they wanted to be taken to the airport and flown to Russia.
The hijackers initially claimed to be Russian, but sources in the Athens prosecutor's office said both men were Albanians with criminal records in Greece. The officials speculated the men tried to hide their identities by pretending to be of a different nationality.
They began releasing hostages in the early afternoon. Some looked dazed and confused as they staggered off the bus. One woman limped toward black-clad anti-terrorist, who waived her to safety.
Premier Costas Caramanlis delayed a trip to a European Union summit in Brussels, Belgium, Thursday to deal with the crisis, his spokesman said. A scheduled demonstration by Greece's main workers union to protest the rising cost of living was also postponed.
Hundreds of thousands of immigrants live in Greece, including many from Albania and the former Soviet Union.
The bus was on a route from the town of Marathon, east of Athens, to the city center. It was hijacked at a stop on a highway renovated for the Olympic Games and used for the marathon race, which follows a 26.2-mile course from ancient Marathon to central Athens.