Osasuna lost the last-16 match 9-0 on January 10 but have been declared winners of the tie on a technicality, with Barcelona striker Geyse having played and scored when she should have been serving a suspension.
In a statement issued on Tuesday, Osasuna said: "The Royal Spanish Football Federation [RFEF] has favourably resolved the claim made by the Osasuna Women's Foundation in relation to the improper team selection committed by Barcelona Football Club in the round-of-16 match of the Copa de la Reina played on January 10 in El Sadar.
"The disciplinary judge has decided 'to give FC Barcelona the game as lost and to consider the tie resolved in favour of CDF Osasuna Femenino'.
"It is possible to file an appeal to the appeals committee against the resolution published this morning by the federal body."
Barcelona, who beat Real Sociedad 3-0 in the Supercopa on Sunday, appear well on course to claim the Spanish league title for a fourth season in a row after winning 14 consecutive games in the competition since the start of the season.
They were defending the Copa de la Reina they won by beating Sporting Huelva 6-1 in last year's final, and reports have said Barcelona, who have also been fined €1,001 by the RFEF, plan to appeal against their expulsion.
Brazilian player Geyse was sent off in her previous match in the competition, playing for Madrid CFF against Sporting in last season's quarter-finals.
Sevilla have also been expelled from this season's cup after Nagore Calderon played in a 1-0 win against Villarreal, when she too had a suspension hanging over her from last season.
The Catalans have won the Spanish league and cup double for the last three seasons, but it emerged they fielded an ineligible player when beating Osasuna 9-0 at the last-16 stage of this season's cup competition.
Osasuna were overpowered on January 10 but have been declared winners of the tie on a technicality, with Barcelona striker Geyse having played and scored when she should have been serving a suspension.
Brazilian Geyse was sent off in her previous match in the competition, playing for Madrid CFF against eventual finalists Sporting Huelva in last season's quarter-finals.
Barcelona believe there are grounds for the ruling to be successfully challenged, with ESPN reporting the club are adamant Geyse was not listed on pre-match lists of disciplinary disqualifications issued by cup organisers the Royal Spanish Football Federation (RFEF).
In a statement issued after Tuesday's expulsion, the Camp Nou giants said: "FC Barcelona announces that the club is to continue to fight for the women's team's rights after they were sanctioned by the competition committee for fielding an ineligible line-up, with an appeal to be presented in due course.
"Should the sanction not be revoked on appeal, FC Barcelona will take every possible action, as it is considered that the line-up ended up being deemed ineligible due to technicalities in this case."
Barcelona, who beat Real Sociedad 3-0 in the Supercopa on Sunday, appear well on course to claim the Spanish league title for a fourth season in a row after winning 14 consecutive games in the competition since the start of the season.
Barcelona have also been fined €1,001 by the RFEF over the ineligibility episode, while Sevilla have been thrown out of this season's cup, too, after Nagore Calderon played in a 1-0 win against Villarreal, when she too had a suspension hanging over her from last season.
Sevilla said they presented arguments against such a punishment but will not appeal any further.
