Obama tapped Fischer, along with former Treasury Department official Lael Brainard, and said he will re-nominate Jay Powell for the seven-member Fed Board.
The Senate confirmed Yellen on Monday. She starts her four-year term on Feb. 1.
The nominations aim to fill slots left open by the departure of Elizabeth Duke, who left in August.
Obama is expected to need to nominate one more Fed governor once the Senate approves current Fed governor Sarah Bloom Raskin to become first woman to hold the No. 2 spot at Treasury.
"These three distinguished individuals have the proven experience, judgment and deep knowledge of the financial system to serve at the Federal Reserve during this important time for our economy," Obama said.
Obama said Fischer "brings decades of leadership and expertise" and "he is widely acknowledged as one of the world’s leading and most experienced economic policy minds."
The president said he is confident that Fischer and Yellen "will make a great team."
Brainard, who left her job at Treasury in November, has served "as one of my top and most trusted international economic advisors during a challenging time not just at home, but for our global economy as well, and her knowledge of international monetary and economic issues will be an important addition to the Fed."
For three years, she served as Treasury’s under secretary for international affairs, from 2010 to 2013. She was responsible for currency policy as well as for coordinating with Group of 20 central banks and finance ministries to slow the European financial crisis and implement financial reforms.
Obama said Powell "has proven to be an effective and wise voice at the Fed."
Powell has been a member of the Fed board since May 2012 but his term is set to expire at the end of January. He worked at Treasury under former President George H.W. Bush.