The two were awarded "for their courageous fight for freedom of expression" in their countries, Chairwoman Berit Reiss-Andersen of the Norwegian Nobel Committee told a news conference.
"At the same time, they are representatives of all journalists who stand up for this ideal in a world in which democracy and freedom of the press face increasingly adverse conditions," she added.
"Free, independent and fact-based journalism serves to protect against abuse of power, lies and war propaganda."
Muratov is editor-in-chief of Russian investigative newspaper Novaya Gazeta, which has defied the Kremlin under President Vladimir Putin with probes into wrongdoing and corruption, and extensively covered the conflict in Ukraine.
When Reuters interviewed him six years ago, his office was across the hall from portraits of six Novaya Gazeta journalists killed since 2001, including Anna Politkovskaya, known for her fearless reporting on Russia's wars in Chechnya, who was shot dead in her stairwell on Putin’s birthday in 2006.
Muratov, 59, is the first Russian to win the Nobel Peace Prize since Soviet leader Mikhail Gorbachev -- who himself helped set up Novaya Gazeta with the money he received from winning the award in 1990.
Ressa, 58, is the first Nobel Peace laureate from the Philippines. She heads Rappler, a digital media company which she co-founded in 2012, and which has grown prominent through investigative reporting, including into large scale killings during a police campaign against drugs.
"Fighting a government is crazy: I didn’t set out to do it, but it became necessary in order to do my job," she wrote in the Financial Times in December.
"I was arrested for being a journalist — for publishing truthful articles unpalatable to those in power — but this has only served to unshackle me, to help me understand what was happening and to chart the path ahead."
The prize is the first Nobel Peace Prize for journalists since the German Carl von Ossietzky won it in 1935 for revealing his country's secret post-war rearmament programme.
In August, a Philippine court dismissed a libel case against Ressa, one of several lawsuits filed against the journalist who says she has been targeted because of her news site's critical reports on President Rodrigo Duterte.
The plight of Ressa, one of several journalists named Time Magazine Person of the Year in 2018 for fighting media intimidation, has raised international concern about the harassment of media in the Philippines, a country once seen as a standard bearer for press freedom in Asia.
In Moscow, Nadezhda Prusenkova, a journalist at Novaya Gazeta, told Reuters staff were surprised and delighted.
"We're shocked. We didn't know," said Prusenkova. "Of course we're happy and this is really cool."
The head of the Nobel committee, Reiss-Andersen, said the committee had decided to send a message about the importance of rigorous journalism at a time when technology has made it easier than ever to spread falsehoods.
"We find that people are manipulated by the press, and ... fact-based, high-quality journalism is in fact more and more restricted," she told Reuters.
It was also was a way to shine a light on the difficult situations for journalists, specifically under the leadership in Russia and the Philippines, she added.
"I don't have insight in the minds of neither Duterte, nor Putin. But what they will discover is that the attention is directed towards their nations, and where they will have to defend the present situation, and I am curious how they will respond," Reiss-Andersen told Reuters.
The Kremlin congratulated Muratov.
"He persistently works in accordance with his own ideals, he is devoted to them, he is talented, he is brave," said spokesman Dmitry Peskov.
The award will give both journalists greater international visibility and may inspire a new generation of journalists, said Dan Smith, director of the Stockholm International Peace Research Institute.
"We normally expect that greater visibility actually means greater protection for the rights and the safety of the individuals concerned," he told Reuters.
The Nobel Peace Prize will be presented on Dec. 10, the anniversary of the death of Swedish industrialist Alfred Nobel, who founded the awards in his 1895 will.