Medics had isolated the patient, reportedly a Nigerian, on Saturday at the Sant Joan hospital in the eastern city of Alicante fearing the presence of the virus, which has killed more than 1,000 people this year.
But the Valencia region health department said in a statement on Sunday that "the samples analysed by the Microbiology Institute have tested negative for the Ebola virus".
The patient is in a "stable" condition in the isolation ward, having been put there pending the test results as a precaution to protect others from a possible contagion of the deadly fever, it said.
A Spanish priest on Tuesday became the first European to die from Ebola during the current outbreak in west Africa, the worst since the disease was first discovered four decades ago.
The 75-year-old missionary, Miguel Pajares, was infected in Liberia, where he worked with infected patients.
Ebola has killed 1,145 people in five months, according to the UN World Health Organization's latest figures as of August 13: 413 in Liberia, 380 in Guinea, 348 in Sierra Leone and four in Nigeria.
There is no widely-available vaccine or medicine for treating Ebola. Pajares was treated with an experimental US serum, ZMapp, while in isolation in a hospital in Madrid.