Palestinians have claimed for years that Israel poisoned Arafat, who died in a French hospital. Israel has denied the charges.
The exhumation marked the end of months of procedural wrangling but only the beginning of the testing. Palestinian officials said it would take at least three months to get results, and even then, they might not be conclusive.
Workers opened Arafat's tomb before daybreak Tuesday, laying bare the remains some four meters (13 feet) below ground level, the Palestinian health minister said. A Palestinian forensics examiner took some 20 samples and handed them to Swiss, French and Russian experts, officials said.
Huge sheets of blue tarpaulin draped over Arafat's mausoleum hid the scene from view, part of an attempt by Palestinian officials to minimize any potential backlash against digging up the grave of Arafat, still widely revered in the Palestinian territories.
By midmorning, the grave was resealed, and Palestinian officials laid wreaths of flowers to signal Arafat's reburial.
The three teams will separately analyze the samples for possible poison, including polonium-210, a lethal radioactive substance first detected in elevated amounts on some of Arafat's clothing this summer.
Polonium disintegrates rapidly, and experts have cautioned that too much time may have passed since Arafat's death to reach a conclusive result.
Polonium was used in the 2006 killing of Alexander Litvinenko, a former KGB officer turned Russian government critic. Litvinenko blamed the Kremlin for poisoning him.
Israel has denied killing Arafat, but many Palestinians believe Israel's then-prime minister, Arafat nemesis Ariel Sharon, had means, motive and opportunity.
Former Sharon spokesman Raanan Gissin said Tuesday that such allegations are baseless and that Israel "had no reason" to kill Arafat, who in his final years lived under Israeli military siege in his walled West Bank compound.
Palestinians launched an investigation immediately after Arafat's death at a French military hospital but made no progress. The dormant probe got a jolt this summer when a Swiss lab found the polonium on Arafat belongings provided by his widow, Suha.
The initial discovery, part of an investigation by the Arab satellite TV station Al-Jazeera, was followed by wrangling between Mrs. Arafat, other relatives and Arafat's successor, Palestinian President Mahmoud Abbas. Mrs. Arafat wanted a quick exhumation, Abbas initially hesitated and Arafat nephew Nasser al-Kidwa said he opposed digging up the remains.
In the end, Abbas could not be seen as blocking a thorough investigation and, armed with blessings from Muslim religious leaders, authorized the exhumation.
Abbas was en route to the United Nations on Tuesday, giving him some distance from the proceedings right outside his office window.
Three different teams were present when the grave was opened Tuesday: one from the Swiss lab, one from France, where an official death inquiry was launched at the request of the widow, and one from Russia, responding to a call for help by Abbas.
Palestinian Health Minister Hani Abdeen told a news conference Tuesday that the remains were four meters (13 feet) below the ground.
Mrs. Arafat, estranged from most of the Palestinian leadership, followed the exhumation from her home in Malta, according to a local newspaper. Mrs. Arafat, who did not consent to an autopsy immediately after her husband's death, told The Times of Malta that her husband's death was the "most important mystery in the Middle East."
Arafat died a month after falling ill at his West Bank compound. The immediate cause of death was a stroke, but the underlying reasons remain unclear, leading to widespread belief in the Arab world that Israel poisoned him.
Medical files released by Palestinian investigators earlier this year portrayed Arafat as a robust 75-year-old whose sudden health crisis was initially blamed on viral gastroenteritis.
Arafat's downward spiral began Oct. 11, 2004, when he vomited after a late supper. His condition deteriorated and two weeks later he was flown to France where he died Nov. 11, 2004.
Dr. Bashir Abdullah, a physician on the Palestinian team of investigators, said Tuesday that Arafat's death "cannot be explained in the framework of disease, and therefore our explanation is that there must have been poisonous material."
Palestinian officials acknowledged Tuesday that they had a long road ahead and that the investigation could hit a dead end.
Tawfik Tirawi, the head of the Palestinian team, said the Palestinians would ask the International Criminal Court to investigate further if there is evidence of poisoning.
Later this week, Abbas is seeking U.N. recognition of "Palestine" as a non-member observer state, an upgrade that could give Palestinians access to the ICC.
Tirawi said previous calls by some high-ranking Israeli officials to get rid of Arafat were an indication that Israel was involved, adding, "we are looking for the evidence."
Former Sharon aides have argued that Israel had no reason to kill Arafat since it had already pushed him aside by confining him to his compound.
For decades, Arafat was the symbol of the Palestinians' struggle for an independent state.
After returning from exile to the Palestinian territories in 1994, as part of interim peace deals with Israel, he zigzagged between leading negotiations with Israel and condoning violence.
Arafat, along with two Israeli leaders, received the Nobel Peace Prize for his commitment to work toward peace with Israel.
He later presided over a violent Palestinian uprising against Israel's occupation of the West Bank, Gaza and east Jerusalem, the territories they seek for a state. As the uprising escalated, Israel confined him to his Ramallah compound.
Arafat also faced criticism at home, where some accused his political circle of corruption and the pocketing of large amounts of aid. But he remains a widely revered figure, and his portrait frequently appears in government offices and street posters.
Associated Press writers Tia Goldenberg in Jerusalem and Dalia Nammari in Ramallah contributed reporting.