The winners were announced Friday by Berit Reiss-Andersen, chair of the Norwegian Nobel Committee.
“Free, independent and fact-based journalism serves to protect against abuse of power, lies and war propaganda,” said Reiss-Andersen.
“Without freedom of expression and freedom of the press, it will be difficult to successfully promote fraternity between nations, disarmament and a better world order to succeed in our time.”
Ressa co-founded news website Rappler in 2012. It has focused “critical attention on the (President Rodrigo) Duterte regime’s controversial, murderous anti-drug campaign,” the Nobel committee said.
She and Rappler “have also documented how social media is being used to spread fake news, harass opponents and manipulate public discourse.”
Muratov was one of the founders of the independent Russian newspaper Novaya Gazeta in 1993.
“Novaya Gazeta is the most independent newspaper in Russia today, with a fundamentally critical attitude towards power,” the Nobel committee said.
“The newspaper’s fact-based journalism and professional integrity have made it an important source of information on censurable aspects of Russian society rarely mentioned by other media,” it added.
Novaya Gazeta is published three times a week and regularly runs investigations into alleged corruption and other malpractice in ruling circles.
Muratov dedicated his award to six contributors to the tewspaper who had been murdered for their work exposing human rights violations and corruption.
“Igor Domnikov, Yuri Shchekochikhin, Anna Politkovskaya, Stas Markelov, Anastasia Baburova, Natasha Estemirova - these are the people who have today won the Nobel Prize,” Muratov said, reciting the names of slain reporters and activists whose portraits hang in the newspaper’s Moscow headquarters.
Alexander Lebedev, the former publisher and a present shareholder of Novaya Gazeta, said: “This is the highest international award one can get personally and as a newspaper.
“It is testimony to the honest service to one’s country that has been shown and achieved through the newspaper’s commitment to reportage, it’s support of human rights, the fight against corruption and the challenging of amorality.
“It must not be forgotten that a huge price has been paid for these principles and this award - tragically, it has been paid for in lost journalists lives.”
In a live broadcast by Rappler, Ms Ressa said she was “in shock”.
She said her win showed that “nothing is possible without facts... a world without facts means a world without truth and trust”.
In a statement, Rappler said it was “honoured and astounded” that its chief executive had been given the prize.
“It could not have come at a better time - a time when journalists and the truth are being attacked and undermined,” it said.
In an interview with the popular Telegram channel Podyom, Mr Muratov said: “I’m laughing. I didn’t expect this at all. It’s madness here.”
He called the prize “retribution for Russian journalism which is being repressed now”.
Kremlin spokesman Dmitry Peskov congratulated Muratov on winning the prize, hailing him as a “talented and brave” person.
“We can congratulate Dmitry Muratov — he has consistently worked in accordance with his ideals, he has adhered to his ideals, he’s talented and brave. It’s a high appraisal and we congratulate him,” Peskov said.
The prize is the first for journalists since the German Carl von Ossietzky won it in 1935 for revealing his country’s secret post-war rearmament programme.
The prestigious award is accompanied by a gold medal and 10 million Swedish kronor (£836,000).
The prize money comes from a bequest left by the prize’s creator, Swedish inventor Alfred Nobel, who died in 1895.
On Monday, the Nobel Committee awarded the prize in physiology or medicine to Americans David Julius and Ardem Patapoutian for their discoveries into how the human body perceives temperature and touch.
The Nobel Prize in physics was awarded Tuesday to three scientists whose work found order in seeming disorder, helping to explain and predict complex forces of nature, including expanding our understanding of climate change.
Benjamin List and David W.C. MacMillan were named as laureates of the Nobel Prize for chemistry Wednesday for finding an easier and environmentally cleaner way to build molecules that can be used to make compounds, including medicines and pesticides.
The Nobel Prize for literature was awarded Thursday to U.K.-based Tanzanian writer Abdulrazak Gurnah, who was recognized for his “uncompromising and compassionate penetration of the effects of colonialism and the fate of the refugee.”
Still to come Monday is the prize for outstanding work in the field economics.