A procedure to remove part of his skull was required to ease pressure on the golfer's brain following complications from surgery on Tuesday, which removed most of a brain tumour.
Doctors at the La Paz hospital took the decision to operate on Ballesteros once more after the condition of the five-time major winner deteriorated, The Telegraph reported.
He lost consciousness after suffering a cerebral oedema, or swelling of the brain. The 51-year-old golfer, who transformed Europe's fortunes in the Ryder Cup, was said to be "stable" after the latest procedure.
In an update on Ballesteros' condition, the Spanish hospital issued the following statement: "Forty-eight hours after his operation, the patient, Severiano Ballesteros, suffered a loss of consciousness because of a cerebral oedema and had to undergo a decompressive craniectomy. The patient is stable and remains under observation in the intensive care unit."
A spokesman for Brain Tumour UK, the charity which provides support for both patients and families, observed that a post-operative craniectomy was usually an emergency procedure.
The need for such an operation happens on average only once in a hundred cases. "The good news is that he's stable," he said, "but there will be a lot of fingers crossed the patient makes a good recovery."
News of the golfer's second surgery of the week came after his brother, Manuel, had earlier expressed hope the operation to remove a brain tumour on Tuesday had been successful.
But the emergence of a subsequent complication, forcing doctors to operate again, clouded those early expressions of positivity.
Concerns about Seve's condition have increased since he first collapsed at Madrid airport last week while waiting for a flight.
The golfer was taken to hospital after suffering a bout of dizziness and loss of consciousness. He announced on Sunday that tests showed he was suffering from a brain tumour.