Savannah Guthrie made the announcement at the top of the "Today" show. "We are devastated," she said.
Later in the day, Variety published a story containing additional sexual harassment allegations against Lauer. The story cited accounts from three unnamed women.
The publication also included allegations that NBC News protected Lauer, citing several woman and saying "they complained to executives at the network about Lauer's behavior, which fell on deaf ears given the lucrative advertising surrounding 'Today.'"
CNN has not independently confirmed the charges. And Lauer has not commented.
"We can say unequivocally, that, prior to Monday night, current NBC News management was never made aware of any complaints about Matt Lauer's conduct," an NBC spokesperson told CNN in the wake of the Variety story.
Lauer's sudden ouster came as a shock to viewers -- but not as a complete surprise to his "Today" show colleagues. They knew that Variety and other news outlets were investigating Lauer's off-camera conduct.
One of those outlets, The New York Times, was in touch with an accuser who then met with NBC lawyers and human resources officials on Monday evening.
The accuser's attorney, Ari Wilkenfeld, said it was a three-hour-long meeting.
"My client detailed egregious acts of sexual harassment and misconduct by Mr. Lauer," Wilkenfeld said.
An investigation ensued on Tuesday. A decision was made to terminate his employment on Tuesday evening -- a swift turnaround time.
NBC News chairman Andrew Lack, a close friend of Lauer's, called and talked with him, according to a source with knowledge of the process.
Lack told staffers on Wednesday morning that Lauer was accepting of the decision and expressed remorse, the source said.
The details of the woman's complaint have not been made public. But Lack said in a memo to staff that "it represented, after serious review, a clear violation of our company's standards."
The source said the woman alleged that the inappropriate behavior began while Lauer was in Russia covering the Winter Olympics in 2014.
An NBC News spokeswoman declined to comment.
Lack's memo said it was the first complaint lodged against Lauer in his career at the network. But it also said "we were also presented with reason to believe this may not have been an isolated incident."
Lack may have been alluding to the ongoing investigations into Lauer's behavior.
Variety reporter Elizabeth Wagmeister said on Twitter that she had been pursuing "serious sexual harassment allegations against Lauer" for two months.
"NBC was aware" of the reporting, Wagmeister tweeted. "There are multiple women we've spoken to with far-ranging accusations against Lauer. The power of journalism has never been more evident with this cultural change."
Lauer's colleagues were visibly shaken up about the firing news on Wednesday's "Today" show. Guthrie, his co-host for the past five years, was told overnight about his termination.
"We were both woken up with the news kind of predawn," Guthrie's co-host Hoda Kotb said. "And we're trying to process it and make sense of it. And it will take some time for that."
The "Today" show is one of the most popular and most profitable franchises on American television. Lauer was the cornerstone of the program for two decades.
The network now has to figure out how to replace him at the anchor desk.
Lauer is the latest high-profile man in media to be brought down by allegations of inappropriate sexual behavior. Just last week, CBS News fired one of its own morning anchors, Charlie Rose, after a report in The Washington Post chronicled years of alleged sexual misconduct on his part.
The torrent began when The New York Times and The New Yorker reported on allegations against the Hollywood producer Harvey Weinstein.
Since then, actors Kevin Spacey and Louis C.K. have been suspended or removed from projects after allegations against them became public. And other prominent journalists, including Mark Halperin of NBC and Michael Oreskes of NPR, have been fired or suspended from their jobs.
Earlier this month, NBC News fired Matt Zimmerman, a top talent booker at the network who worked at "Today," over allegations of "inappropriate conduct."
Zimmerman declined to comment on Wednesday.
The firing of Lauer removes one of the most recognizable personalities on television at a time when morning news programs are increasingly important to network news divisions.
"This is a sad morning at 'Today' and NBC News," Guthrie said at the top of the 7 a.m. hour. "As I'm sure you can understand, we are devastated. I'm heartbroken for Matt."
Guthrie also said she was heartbroken for the woman who accused Lauer of misconduct, noting "it's long overdue" that women feel comfortable coming forward against abusive men.
Kotb, on the set with Guthrie, said she has known Lauer for years and "loved him as a friend and a colleague."
"It's hard to reconcile the man who walks in every day" with the person who was identified in the complaint, she said.
Lauer, 59, was named a co-anchor of "Today" in January 1997 after three years as the newsreader.
He co-anchored NBC's coverage of the September 11, 2001 terrorist attacks and other historic news events.
His contract calls for him to be paid tens of millions a year. It reportedly ran through 2018.
--CNNMoney's Jill Disis, David Goldman and Chris Isidore contributed to this report.
Brian Stelter and Tom Kludt, CNN Money
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