Garitano hadn't coached since being fired from Real Sociedad last year after managing the team for only half a season. He had been with Madrid club Leganes from 2013-2018, leading the team from the third division to the top flight.
Fernández said at a news conference on Monday he decided to resign because he felt he "would not be at 100 percent next season." He joined Alaves at the end of 2017, helping the team finish 14th in the league last season, comfortably escaping relegation.
Alaves had a surprising start to this season, being as high as second in the standings and remaining in the fight for the final Champions League place until about 10 rounds to go.
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