Three other people, including the nurse's husband, have been quarantined.
The European Commission has asked Spain to explain how the nurse could have become infected.
Some 3,400 people have died in the outbreak - mostly in West Africa.
The Spanish auxiliary nurse, a 40-year-old woman who has not been named, was one of about 30 staff at the Carlos III hospital in Madrid who had been treating priests Manuel Garcia Viejo and Miguel Pajares, officials say.
Mr Garcia Viejo, 69, died at the hospital on 25 September after catching Ebola in Sierra Leone. Mr Pajares, 75, died in August after contracting the virus in Liberia.
The nurse had twice gone into the room where Mr Garcia Viejo had been treated, to be directly involved in his care and to disinfect the room after his death. Both times she was wearing protective clothing.
Madrid healthcare director Antonia Alemany told reporters that according to the information available: "The nurse went into the room wearing the individual protection gear and there's no knowledge of an accidental exposure to risk."
Shortly afterwards the nurse went on holiday, a hospital spokesman said, but fell ill on 30 September and was admitted to Alcorcon hospital in south-west Madrid on Sunday after being tested positive for Ebola.
Early on Tuesday she was moved under police escort to Carlos III hospital in the capital and is said to be in a stable condition.
The Spanish health authorities say she is being treated with a drip using antibodies from previous Ebola patients.
Her husband and a second nurse who treated the missionary are now in quarantine, officials said, as well as a man who recently arrived on a flight from Nigeria.
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