"He was in a very bad condition when he arrived," neurosurgeon Salah Abdel-Khalek told an Egyptian radio station Monday.
"The footballer had serious damage to his spinal column between the fifth and sixth vertebrae, a blow to the spinal cord, breathing difficulties and brain bleeding, but the surgery was successful.
"He will remain in intensive care for two days, where he is currently using a ventilator," the surgeon added.
Bhebey-Ndey, a 25-year-old striker from the AC Leopards club, was injured when tackled by the goalkeeper of Egyptian club Zamalek during a CAF Confederation Cup game.
An official from Zamalek, who won the group-stage match 2-0 in Cairo, said his club would pay the medical expenses.
Competition organisers, the Confederation of African Football said in a statement: "CAF wishes a speedy recovery for Rudy Ndey after his injury against Zamalek."