The Spanish side sit rock-bottom of La Liga with 12 points from 17 matches, though just three points off the tip of the relegation zone.
The former Tenerife boss guided Deportivo back to the top flight in the 2011-12 season but has struggled to string victories together this campaign, and Augusto Cesar Lendoiro insisted that change is necessary.
"It's a decision that didn't come today, it was taken before the assembly following the defeat against Espanyol [on December 20]," the president told reporters at a press conference on Sunday.
"The situation became irreversible. We're not fans of changing the coach, but a shake-up was needed that had to come from this, because you don't have other options to make changes in the team."