The Times and The Washington Post took the award in the national reporting category for their coverage of Russian meddling in the 2016 U.S. presidential election and contacts between President Donald Trump's campaign and Russian officials.
The Press Democrat of Santa Rosa, California, received the breaking news reporting award for coverage of the wildfires that swept through California wine country last fall, killing 44 people and destroying thousands of homes.
The Washington Post also won the investigative reporting prize for revealing decades-old allegations of sexual misconduct against Senate candidate Roy Moore of Alabama. The Republican former judge denied the accusations, but they figured heavily in Doug Jones' victory as the first Democrat elected to the Senate from the state in decades.
One of the biggest surprises of the day came in the non-journalism categories when rap star Kendrick Lamar was awarded the Pulitzer for music, becoming the first non-classical or non-jazz artist to win the prize.
The Pulitzers, American journalism's most prestigious awards, reflected a year of unrelenting news and unprecedented challenges for U.S. media, as Trump repeatedly branded reporting "fake news" and called journalists "the enemy of the people."
The New York Times won three Pulitzers and The Washington Post and Reuters received two apiece.
In announcing the journalism prizes, Pulitzer administrator Dana Canedy said the winners "uphold the highest purpose of a free and independent press, even in the most trying of times."
"Their work is real news of the highest order, executed nobly, as journalism was always intended, without fear or favor," she said.
A string of stories in The Times and The Washington Post shined a light on Russian interference in the presidential election and its possible connections to the Trump campaign and transition - ties now under investigation by special counsel Robert Mueller. The president has called the investigation a "witch hunt."
The Pulitzer judges commended the two newspapers for "deeply sourced, relentlessly reported coverage in the public interest."
In stories that appeared within days of each other in October, The Times and The New Yorker reported that movie mogul Weinstein faced allegations of sexual harassment and assault from a multitude of women in Hollywood and had secretly paid settlements to keep the claims from becoming public.
The Pulitzer judges said The Times' reporters, led by Jodi Kantor and Megan Twohey, and The New Yorker's Ronan Farrow produced "explosive, impactful journalism that exposed powerful and wealthy sexual predators" and forced the issue of sexual abuse into the open.
"By revealing secret settlements, persuading victims to speak and bringing powerful men to account, we spurred a worldwide reckoning about sexual abuse that only seems to be growing," New York Times executive editor Dean Baquet said in remarks to the newsroom.
"People have been saying for decades that this kind of behavior is endemic in society," New Yorker editor David Remnick said, adding that he hoped the stories would "help not only bring it to light but change the culture."
Weinstein was ousted from the studio he co-founded and now faces criminal investigations in New York and Los Angeles. He has apologized for "the way I've behaved with colleagues in the past" but denied any non-consensual sexual contact.
The stories' impact spread beyond Weinstein to allegations against other powerful men in entertainment, politics and other fields, toppling such figures as "Today" show host Matt Lauer, actor Kevin Spacey, newsman Charlie Rose and Sen. Al Franken. Men and women, famous or not, have spoken about their own experiences with sexual harassment and assault in what has become known as the #MeToo movement.
"This moment gets called a reckoning, but we just started telling the truth about old abuses of power," Farrow tweeted Monday.
Weinstein spokeswoman Holly Baird declined to comment on the Pulitzer except to suggest similar recognition should be given to Tarana Burke, an activist who founded the #MeToo movement on Twitter about a decade ago to raise awareness of sexual violence.
In other categories, the Arizona Republic and USA Today Network won the explanatory reporting prize for a multi-format look at the challenges and consequences of building the Mexican border wall that was a centerpiece of Trump's campaign. The project included footage from a helicopter flight along the entire 2,000-mile border.
The local reporting award went to The Cincinnati Enquirer for what the judges called "a riveting and insightful" narrative and video about the heroin epidemic in the area. More than four dozen reporters and photographers dove into the drug's toll over one week.
Clare Baldwin, Andrew R.C. Marshall and Manuel Mogato of Reuters won the international reporting award for their coverage of Philippines President Rodrigo Duterte's deadly crackdown on drugs, and the news agency's photographers received the feature photography prize for their images of the plight of Rohingya refugees who have fled Myanmar.
The breaking news photography award went to Ryan Kelly of The Daily Progress of Charlottesville, Virginia, who captured the moment a car plowed into counter-protesters demonstrating against a white nationalist rally in the college town. The car killed counter-demonstrator Heather Heyer.
Kelly made the photo on his last day at the newspaper before moving on to a job at a brewery. In a text Monday, Kelly described the prize as an "incredible honor" but added: "Mostly I'm still heartbroken for Heather Heyer's family and everybody else who was affected by that tragic violence."
Rachel Kaadzi Ghansah, a freelance writer for GQ magazine, took the feature writing award for a profile of Dylann Roof, the avowed white supremacist convicted of killing nine black churchgoers in Charleston, South Carolina.
The commentary award went to John Archibald of Alabama Media Group in Birmingham, Alabama, for pieces on politics, women's rights and other topics. Art critic Jerry Saltz of New York magazine won the criticism award .
Andie Dominick of The Des Moines Register received the editorial writing prize for pieces about the consequences of privatizing Iowa's administration of Medicaid.
Freelance writer Jake Halpern and freelance cartoonist Michael Sloan were awarded the editorial cartooning prize for a graphic narrative in The New York Times about a family of refugees fearing deportation.
The Pulitzers were announced at Columbia University, which administers the prizes. This is the 102nd year of the contest, established by newspaper publisher Joseph Pulitzer.
Winners of the public service award receive a gold medal; the other awards carry a prize of $15,000 each.
Associated Press writers Justin Lynch and Colleen Long in New York and Ben Finley in Norfolk, Virginia, contributed to this report.
Copyright 2018 The Associated Press. All rights reserved. This material may not be published, broadcast, rewritten or redistributed.