A representative for the Spanish musician, who is Penelope Cruz's brother, confirmed the sad news.
The couple were rumoured to have split in March, just a month after their first anniversary.
But they were soon spotted back in each other's arms, on a string of dates.
Just last month, the actress said: "I'm in love. I'm a hopeless romantic."
Thirty-seven-year-old Eva began dating Eduardo, 27, just months after her divorce to basketball player Tony Parker was finalised.
Earlier this year she told Spanish Vanity Fair: "I was very lucky to find Edu".
Before Tony, Eva was married once before, to General Hospital actor Tyler Christopher. Their two-year marriage ended in 2004.