Rubiales forcibly kissed Jenni Hermoso after Spain's women's team won the World Cup, beating England in the final.
There has since been a major backlash to Rubiales, and Spain's players agreed to boycott playing for the national team until fundamental changes were made to the federation's (RFEF) structure.
Players were called up for a national team camp, however, ahead of their clash with Sweden, and talks between the squad and the RFEF, which lasted for seven hours, have led to an agreement to end the boycott.
However, the Spanish FA had promised to make "immediate and profound" changes to their structure, and that appears to have directly led to the firing of Camps.
The squad, per Sport, had requested his removal, and they also claim that he is Rubiales' "right-hand man" within the RFEF.
The federation issued a statement, which read: "RFEF dispenses with the services of the general secretary, Andreu Camps.
"The Federation will not appoint a new general secretary and the functions will be assumed on an interim basis by Elvira Andrés and Alfredo Olivares until the end of the electoral process."
A total of 21 of the 23 players called up have remained in the squad, but Patri Guijarro and Mapi Leon both opted to leave.
Spain play Sweden on Friday in their first game of the Nations League.