Arthur Sulzberger Jr., the newspaper's publisher and chairman of its parent company, called Baquet the best qualified journalist to take on the job in the Times' newsroom.
"He is an exceptional reporter and editor with impeccable news judgment who enjoys the confidence and support of his colleagues around the world and across the organization," Sulzberger said in a statement.
Sulzberger added that Baquet was closely involved with Abramson in the Times' digital transformation over the past six months.
The managerial change came with little warning or explanation to Times employees, according to several staffers. Workers were sent an email Wednesday afternoon that asked them to gather in the newsroom. There, less than ten minutes later, publisher Arthur Sulzberger Jr. introduced Baquet as the Times' new executive editor.
According to one staffer, Sulzberger said a concern about newsroom management led to the change. Staffers applauded Baquet's promotion. Abramson was not present at the gathering.
Abramson, 60, was the paper's first female executive editor. She joined the newspaper in 1997 after working for nearly a decade at The Wall Street Journal. She was the Times' Washington editor and bureau chief before being named managing editor in 2003.
"I've loved my run at The Times," Abramson said in the company's statement. "I got to work with the best journalists in the world doing so much stand-up journalism."
Baquet succeeded her as managing editor after she was named to the top editing spot.
New York Times Co. shares fell 71 cents, or 4.5 percent, to end the regular trading session at $15.06.
Michael Sisak contributed to this report.