The only "no" vote was cast by Sen. Bernie Sanders, Ind-Vt., Crain's Chicago Business reported.
In a statement issued by the White House, Obama commended the bipartisan vote and called Pritzker "a proven leader, a successful entrepreneur, and one of the most accomplished and highly respected women in business today."
"She knows what it takes to build companies from the ground up, and she shares my belief in doing everything we can to help businesses and workers succeed and make America a magnet for good jobs," the president said. "Penny will be a key member of my economic team as we continue to work to grow our economy and strengthen the middle class."
Sen. Dick Durbin, D-Ill., said in a statement Pritzker -- who is from Illinois -- "has a proven track record in promoting jobs and growth, and I look forward to working with her as she continues lead our country towards economic recovery as our next Secretary of Commerce."
The department promotes U.S. exports and conducts the U.S. Census.
Pritzker's nomination came in for criticism from organized labor due to treatment of employees of Hyatt Hotels Corp., which her family owns, Crain's said.
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