Murphy is now resting at a hospital in New York City, Lt. Gov. Sheila Oliver said.
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Oliver is serving as New Jersey's acting governor while Murphy recovers.
The surgery followed Murphy's announcement on Twitter last month that he had a tumor on his left kidney and planned to undergo a partial nephrectomy to remove it.
"The prognosis is very good and I'm profoundly grateful to my doctors for detecting the tumor early," Murphy said at the time.
Murphy, a Democrat, said in his recent budget address that he was overwhelmed and thankful for an outpouring of encouragement since news of the tumor became public.
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Ninety percent of such tumors are cancerous, Murphy's office said, but doctors won't be able to tell for sure until the surgery.
Ahead of the surgery, Murphy told NJ Advance Media that doctors are confident of being able to eradicate it. He said he didn't anticipate needing chemotherapy or radiation.
The Associated Press contributed to this report.