A 3-0 loss at Real Sociedad on Sunday left Mallorca 19th in the table and prompted the sacking of Caparros, who had been in charge since October 2011.
Acting president Llorenc Serra Ferrer thanked the 55-year-old for his service and insisted that the club would not act hastily in appointing a successor.
He said: "I respect Caparros so much. I know that we have sacked a great coach. I would like to thank Joaquin and his coaching staff for their honour, dedication, desire and for helping the club grow in every sense.
"We talked a lot about the situation that the team was in and we reached the conclusion that something was needed to to give us a lift for the rest of the season and achieve our aim of staying in the division.
"We have opened channels to talk with some trainers, but we do not have a name. Now we do not want to take such an important decision in a hurry and there are still 48 points to play for."
Caparros has previously had managerial spells at Sevilla, Athletic Bilbao and Deportivo La Coruna.