The delicate procedure was performed 24 hours later than scheduled owing to a slight infection in his respiratory tract. The hospital had said the surgery would be conducted only after the infection cleared up.
"The operation Mr Sharon was supposed to undergo yesterday was conducted today (Wednesday) and was successfully completed a short while ago," the Hadassah hospital said in a statement.
"The prime minister is being taken back to his room in the intensive care unit," it added, providing no further details immediately.
The segment of skull was removed in brain surgery following his debilitating stroke on January 4 that has left the 78-year-old legendary statesman bed-ridden and comatose ever since in the renowned Jerusalem hospital.
Doctors are understood to be preparing long-term care plans for Mr Sharon and although the hospital has not announced a final decision, discussions have continued on where the premier will reside in the future.
Olmert takes the reins
The operation came one day before Mr Sharon's former deputy Ehud Olmert, who led their centrist Kadima party to a narrow victory in last week's general election, is set to be tasked with forming Israel's next coalition government.
On Sunday, the outgoing Israeli cabinet is expected to pronounce Mr Sharon permanently rather than temporarily incapacitated and Mr Olmert, currently acting prime minister, officially declared head of government.
The move will be a mere formality because Mr Olmert is set to be given the task by President Moshe Katsav of forming the next coalition government after Kadima won the highest number of parliamentary seats in March 28 polls.
Mr Sharon's crowning achievement of his career was taking Israel out of the Gaza Strip last September after 38 years set the precedent for vacating occupied Palestinian territory.
It was Mr Sharon, not Mr Olmert, had been expected to lead Kadima to victory in the election had his brain haemorrhage not drawn a dramatic line under his career.
It was his decision to form Kadima last November that triggered a complete turnaround in Israeli politics when he quit the right-wing Likud party.
Mr Sharon’s departure dealt a massive blow to the once dominant Likud, which suffered a humiliating defeat in the March 28 election, embittered by its opposition to the Gaza pullout and the prospect of more West Bank withdrawals.
Mr Sharon was induced into a coma as part of his treatment for the brain haemorrhage but he has yet to regain consciousness despite responding to initial pain stimulus tests.