Retired Army Lt. Gen. Keith Kellogg was named acting national security adviser to replace Flynn, who admitted in his resignation letter that he "inadvertently" gave "incomplete information" about multiple calls with the ambassador.
Flynn previously denied that he spoke with the ambassador in December about sanctions the U.S. imposed on Russia for its suspected interference in the 2016 presidential election — an act that may have violated federal law. Vice President Mike Pence repeated the denial when asked about the situation in January, but administration officials noted that he was relying on information provided to him by Flynn.
Sources in the administration confirmed that the Justice Department, under the direction of then-acting Attorney General Sally Yates, informed the White House in January that Flynn may have misled Pence and other senior officials about his communications with the ambassador.
Trump fired Yates, an Obama administration appointee, on Jan. 30 after she instructed the Justice Department not to defend his controversial executive order limiting travel and immigration from seven majority-Muslim countries in Africa and the Middle East.
In a statement announcing her dismissal, the White House said Yates "betrayed the Department of Justice" and said she was "weak on borders and very weak on illegal immigration."
Sources told ABC News on Monday that Flynn called Pence on Friday to apologize for misleading him about his conversation with the ambassador.
Authorities are investigating communications between Flynn and Russian officials but have not yet found clear evidence of wrongdoing.
In his resignation later, Flynn — announced as Trump's pick for the position on Nov. 18 — cited the "fast pace of events" for "inadvertently" briefing "the vice-president-elect and others with incomplete information regarding my phone calls with the Russian ambassador.”
Flynn said that in his role as incoming national security adviser during the transition, he "held numerous phone calls with foreign counterparts, ministers and ambassadors ... to facilitate a smooth transition and begin to build the necessary relationships between the president, his advisors and foreign leaders," according to the letter.
In his resignation letter, Flynn noted that he apologized to Trump and Pence and that they accepted the apology.
"Throughout my over 33 years of honorable military service and my tenure as the national security advisor, I have always performed my duties with the utmost of integrity and honesty to those I have served, to include the president of the United States," wrote Flynn.
"I am tendering my resignation, honored to have served our nation and the American people in such a distinguished way."
ABC News' Jonathan Karl and Pierre Thomas contributed to this report.
This is a developing story. Please check back in for updates.