The club decided to act after Sunday's 2-0 defeat at home to Girona left them second bottom in the second tier with just one win from seven games.
Esnaider took over in April but his first game in charge - a 5-1 home defeat by neighbours Real Madrid - set the tone with the Argentine unable to propel the club away from the relegation zone and they finished 19th.
A promotion challenge was expected this term but it has thus far not materialised, resulting in Esnaider's dismissal on Monday.
A club statement read: "It has been decided to dismiss Juan Esnaider as coach.
"Everyone at Getafe appreciates his work and we wish him well in his future career."