Ballesteros will remain there until next week to see if the tumour is malignant.
Medics were due to only remove tissue from the growth on Tuesday morning. But they ended up taking out the entire tumour after agreeing it was the best course of action.
A statement released by La Paz Hospital said: "The operation concluded without complications. He is currently conscious, although he will not be able to receive visits over the next few days until he has recovered from surgery."
Ballesteros was admitted to hospital last week after collapsing at an airport. Doctors revealed he had suffered an epileptic attack caused by the tumour.