Jerusalem's Hadassah Medical Centre announced late Sunday that the procedure had been "completed successfully."
Justice Minister Yariv Levin, a close ally, served as acting prime minister during the operation. Netanyahu,75, is expected to remain hospitalised for several days.
With so much at stake, Netanyahu's health in wartime is a concern for both Israelis and the wider world.
As Israel's leader, Netanyahu is at the centre of major global events that are shifting the Middle East. With the dizzying pace of the past 14 months, being incapacitated for even a few hours can be risky.
He will be in hospital at a time when international mediators are pushing Israel and Hamas to reach a ceasefire in Gaza and as fighting between Israel and Yemen's Iran-backed Houthi rebels intensifies.
The judges overseeing Netanyahu's trial accepted a request from his lawyer to call off three days of testimony scheduled this week.
The Israeli prime minister has had a series of health issues in recent years, but has gone to great lengths to bolster a public image of himself as a healthy, energetic leader.
But that image was shattered last year when Netanyahu's doctors revealed he had a heart condition, a problem that he had apparently long known about but concealed from the public.
The revelation came as Netanyahu was dealing with massive anti-government protests. The news about a chronic heart problem stoked further anger and distrust during extreme political polarisation in Israel.
Later in the year, Netanyahu was rushed to the hospital for what doctors said likely was dehydration. He stayed overnight, prompting his weekly Cabinet meeting to be delayed.
Earlier this year, Netanyahu underwent hernia surgery, during which he was under full anesthesia and unconscious. Levin served as acting prime minister during the operation.
According to Netanyahu's office, the Israeli leader was diagnosed with a urinary tract infection on Wednesday stemming from a benign enlargement of his prostate. The infection was treated successfully with antibiotics, but doctors said the surgery was needed in any case.
Netanyahu is among older world leaders including US President Joe Biden, 82, President-elect Donald Trump, 78, and Pope Francis, 88, who have come under scrutiny for their age and health issues.
