Sharon, 77, was rushed into surgery on Saturday morning after an abdominal scan revealed dead tissue in his digestive system.
Doctors removed 50 centimetres, or one-third, of his large intestine during the four-hour surgery, the seventh operation Sharon has undergone since suffering the stroke on 4 January.
The dead tissue was caused by infection or a drop in the blood supply to the intestines, something common in comatose patients, Sharon's doctors said.
"Prime Minister Ariel Sharon's condition stabilised after surgery, but it is still described this morning as critical and stable," according to the statement from Hadassah Hospital in Jerusalem. "The prime minister is in the general intensive care unit."
Though the surgery was successful, Sharon's doctors said hope was fading for the premier to wake from his coma.
"Prime Minister Ariel Sharon's condition stabilised after surgery, but it is still described this morning as critical and stable"
Since the stroke, Sharon has been hooked up to a breathing tube. A feeding tube was inserted in his stomach on 1 February.
Sharon was Israel's most popular politician before he fell ill.
He pulled Israel out of the Gaza Strip last summer and redrew Israel's political map late last year by leaving his hardline Likud party and forming the centrist Kadima.
Ehud Olmert, the acting prime minister, has taken over as head of Kadima and worked hard to paint himself as Sharon's political heir ahead of 28 March elections.
Speaking to Kadima members on Sunday night, Olmert praised Sharon's "greatness" in following through with the Gaza pullout in the face of strong opposition.
"He came up with the initiative, took the responsibility, marked the goals, took the risks and won thanks for all that," Olmert said. "We will continue this way."
Despite Sharon's illness, polls show Kadima receiving twice as many seats in the 120-member Israeli parliament as its nearest rivals.
Sharon's son Omri has to give
permission for any treatment
Earlier on Sunday, before the weekly Cabinet meeting, Olmert said he was relieved by the success of Sharon's surgery and expressed his support for Sharon's sons, Omri and Gilad.
"We are encouraged by the reports from Hadassah Hospital regarding the health situation of the prime minister following the operation yesterday," Olmert said. "The whole government is sending a warm hug to Omri and Gilad, who are standing by their father day and night."
Sharon's sons have acquired guardianship over the prime minister since his stroke. Under Israeli law, any decision to perform emergency surgery or to discontinue medical treatment would require their consent, said Jonathan Davies, a leading Israeli medical law expert.