"No society can be free and fair without journalists who are able to investigate wrongdoing, bring information to citizens, hold leaders accountable and speak truth to power," he said.
The UN chief voiced alarm at growing attacks against the media, both online and in person and especially targeting women journalists, as well as the rise in disinformation.
"This cannot become the new normal," he said.
In Washington, a State Department spokesperson congratulated the two winners and said that "freedom of expression remains under threat in many parts of the world."
He said the United States will "stand in solidarity with independent journalists in Russia" after the prize was co-won by Muratov, the chief editor of the Novaya Gazeta newspaper whose top investigative reporter, Anna Politkovskaya, is one of six journalists and contributors killed for their work since 2000.
"The United States has deep admiration for the bravery and integrity of the journalists of Novaya Gazeta, who under Mr Muratov's leadership continue to report the truth in the face of serious threats," the spokesperson said.
Ressa, who also holds US citizenship, is co-founder of Rappler, a digital media company for investigative journalism who has faced criminal charges after stories critical of Philippine President Rodrigo Duterte including his bloody drug war.
"We commend Ressa's long-standing dedication to safeguarding freedom of expression for all journalists both in the Philippines and in the world," the spokesperson said.
"Her tireless work to promote freedom of expression comes at a time when liberty of the press is increasingly under threat."