The vote was along party lines, with Price being confirmed by a 52-47 margin.
Price, a Republican from Georgia, has pushed to undo the Affordable Care Act and has advocated making major changes to Medicare, stances that Democrats have opposed.
Republicans say Price is a champion of free market principles who will guide the repeal and replace of Obamacare, the top legislative priority for President Donald Trump and Congressional Republicans.
The Senate worked late because of procedural delays pressed by Democrats on a series of Trump's Cabinet members.
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