The narrowest margin previously was an 84-16 vote for former Fed Chairman Paul Volcker in 1983, The Wall Street Journal reported.
Sen. Jim Bunning, R-Ky., called the vote a referendum on bailouts in a strange turnaround that had Republicans arguing to defeat Bernanke, who was chairman of President George W. Bush's Council of Economic Advisers before Bush nominated him to replace longtime Chairman Alan Greenspan in 2006.
Democrats argued a new Fed chairman at this time would create instability in the country's economic recovery, which Bernanke has called "nascent."
"To vote against confirmation could unnerve investors and exacerbate economic uncertainty in the marketplace, which is exactly what we do not need at this time," said Sen. Robert Menendez, D-N.J.
The debate characterized the vote as a referendum on many of the country's economic policies, from supervision of banks to bailouts to anger at huge bank bonus checks.
The vote "puts economic policy squarely in people's minds," said Sen. Jeff Merkley, D-Ore.
President Barack Obama said he was gratified by the Senate confirmation.
"As the nation continues to face the consequences of the worst recession in a generation, Ben Bernanke has provided wisdom and steady leadership in the midst of the financial and economic crisis," Obama said in a statement issued by the White House. "While the worst of the storm has passed, its devastation remains and we have a lot of work to do to rebuild our economy."