The defeat, which was the club's 15th in the league this season, left Los Che in ninth position in the table with just one game remaining.
"This is not the season we wanted," he told reporters at a press conference.
"We had no intention of playing this sort of campaign. Now, we have to finish in the best way possible and start thinking about next year.
"I'm the coach and I have to take responsibility for what's happened."
Valencia reached the semi-finals of the Europa League this season, but lost out to Sevilla.