A final day victory over already-relegated Real Betis was not enough to save Osasuna, as Almeria's draw with Athletic Bilbao moved them one point clear of trouble.
And Gracia, who only took the reins at Estadio El Sadar in September, has chosen to resign after failing to keep the club in the top flight.
"After a meeting with the president I have decided not to continue," he said on Wednesday. "I wanted to stay for my whole life but circumstances dictate that is not good for me or the club.
"It has been a very intense process and has been a major burnout.
"I consider myself responsible for all my work, team play and points earned. I believe that with a little more luck we could have achieved the objectives.
"I wish all the best to Osasuna."
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