The 52 to 47 vote was along party lines.
Democrats opposed Price, a Republican from Georgia, because he is a key architect of undoing the Affordable Care Act and has advocated making major changes to Medicare.
Their suspicions were deepened when it was revealed Price traded health care stocks while having oversight duties of the health care industry. Price has consistently denied any wrongdoing.
Republicans view Price, an orthopedic surgeon, as 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.