Doctors at Howard University Hospital spent more than eight hours repairing damage linked to radioactive seeds implanted in the minister's prostate following his 1991 cancer diagnosis.
"It was a difficult operation because of the type of scarring that's there," said Dr. Debra H. Ford, chief of surgery at the hospital.
Ford led a team of surgeons who removed Farrakhan's rectum and temporarily rerouted his urinary tract.
"He's talking and joking," said Ford, characterizing his condition as stable. He is expected to spend at least 10 days in the hospital.
Although doctors had known about the problem for some time, the operation was delayed until after last month's "Million Family March" in Washington. Farrakhan, 67, delivered a nearly three-hour keynote address during the event. Doctors said his medical condition did not cause him any discomfort or fatigue before his hospitalization.
In April of last year, Farrakhan underwent surgery at Howard after potentially life-threatening hemorrhaging occurred at the site of a rectal ulcer linked to his cancer treatment.
Farrakhan is expected to return to Howard for periodic checkups following his release. He will also have to undergo a procedure early next year to restore his normal urinary function.
Although doctors believe Farrakhan is free of cancer, tissue samples removed during the surgery will be submitted to a pathologist for testing, Ford said.