Spiegel Online, where Moore was previously employed, published the news on Tuesday after Germany's foreign ministry confirmed that, "a German citizen, who also has US citizenship and was kidnapped in Somalia, was freed today."
The spokeswoman declined to provide further details, notably whether the 45-year-old was freed by his captors, escaped or was liberated by force.
He was flown to Somalia's capital in Mogadishu and taken to a safe place where he will have a medical and psychological assessment.
Moore was kidnapped by pirates in January 2012 in the town of Galkayo while in Somalia researching for a book on piracy. He is said to be in good health, considering the circumstances.
The German and American foreign offices, as well as Moore's family and friends, worked to secure his release.
A Somali pirate source, who asked not to be named, told AFP a ransom was paid.
Der Spiegel’s editor-in-chief Wolfgang Büchner said: "We never gave up hope and are happy for Michael and his mother Marlis for whom this nightmare is finally over."
Friends and colleagues took to Twitter upon hearing the news. "Journalist (and friend) Michael Scott Moore freed after 976 days in captivity. Relieved he's coming home," said Berlin-based friend and fellow writer Andrew Curry.
Just learned that my good friend Michael Scott Moore was released after 2.5 years of captivity in Somalia. Apparently in good shape.— Charles Hawley (@charles_hawley) September 23, 2014
Friend and one-time Der Spiegel colleague Daryl Lindsey called the mood, "deep, deep elation" on Twitter.
Moore had worked for Spiegel Online both as a staff member and a freelancer. He was working with Spiegel on a freelance basis before he left for Somalia.
Moore's best-known work is a 2010 book on the history of surfing called, "Sweetness and Blood: How Surfing Spread From Hawaii and California to the Rest of the World, With Some Unexpected Results." He told the New York Times his curiosity was piqued when he discovered the man who first brought surfing to Germany and researched the phenomenon of river surfing at Munich's standing wave.
His next project would build on a series of articles he wrote on Somali piracy, he told the Times. "A book about piracy has the same appeal to me as the surf book — it has the same clash between hard fact and clichéd mythology. It would also involve a great deal of travel," said Moore.
His travels were cut short almost three years ago. About four months after he was kidnapped, a video was published online where Moore responds to questions from his apparent captors, some of whom stand behind him pointing what appear to be a machine gun and a grenade launcher.
"I'm afraid. I'm terrified," says Moore in the video.
Moore's time in captivity was marked by a relative absence of media coverage, which Robert Maloney, press freedom advocate and director of the Committee to Protect Journalists, called a "news blackout" on Twitter.
Writing on the platform Medium.com, bloggers War Is Boring, said the silence in such cases is intended to protect the family of the hostage and reduce the spotlight on the kidnapping, so as to give the kidnappers less leverage to negotiate a high ransom for a hostage that appear to be valuable. In keeping with the apparent strategy, even in Tuesday's foreign ministry statement, Moore was not directly named.
Still, a person familiar with the situation, said there was a lot of work from a lot of people going on behind the scenes and that in no way had Moore been forgotten.
Der Spiegel reported that the Pulitzer Center on Crisis Reporting, which had financially supported Moore's research trip to Somalia, was greatly relieved. "We're grateful to all the people who have worked so long to bring about Michael's release - and thrilled that he and his family can be reunited at last," said the center's director Jon Sawyer.
Deaths in Yemen
But two German Christian aid workers and their son, who were kidnapped five years ago in Yemen have died, a relative said on Tuesday.
The couple, identified as technician Johannes Hentschel and his wife Sabine, then both aged 35, and their three young children were abducted in June 2009 in northern Yemen.
Two of the children, both girls, were freed in May 2010, but the parents and their then one-year-old son have since died, the father's brother-in-law, Christian pastor Reinhard Pötschke, said citing a letter from the foreign ministry.
Their young son is believed to have died from an infection. It is unclear how the parents died.
The news confirmed the family's worst fears, but Pötschke said there was also some relief that they could now start mourning.
Several other foreigners were abducted with the family by kidnappers believed to have links to Al-Qaeda.
The two girls, now aged eight and 10, live with relatives in the family's home state of Saxony in eastern Germany.