Barcelona signed the two players in the close season but due to the club being unable to meet LaLiga's wage cap, they were allowed to be registered for the first half of the season only.
On Saturday, the Spanish football federation (RFEF) and LaLiga had rejected a request to register them both for the second half of the season.
Spain's Consejo Superior de Deportes (CSD), an autonomous government agency that oversees sport, on Wednesday stayed that ruling.
"This measure, which is provisional until the final resolution of the appeal lodged by the club and the aforementioned players, suspends the Agreement of the Monitoring Committee of the RFEF-LaLiga Coordination Agreement... and the cancellation of the sporting licences of the aforementioned players," it said.
"Likewise, it maintains the validity of those licences until this appeal is finally resolved."
Two courts had also previously rejected Barcelona's requests but the CSD upheld the club's appeal, stating that professional athletes "have the right to a sporting career in accordance with their potential with guarantees and certainty."
The CSD also took into account the "economic and sporting consequences" for the club and players, and "the interests" of the Spanish national team and domestic competitions.
The verdict came after coach Hansi Flick announced Barcelona's matchday squad for their Spanish Super Cup semi-final against Athletic Bilbao later on Wednesday, with both players omitted.
Barcelona's Lamine Yamal scored to help put his side into a third straight Spanish Super Cup final. (AP PHOTO)
Meanwhile in the Spanish Super Cup semi-final, goals from Gavi and Lamine Yamal earned Barcelona a 2-0 win over Athletic Bilbao in Jeddah.
After creating plenty of early chances, Barcelona took the lead in the 17th minute through Gavi, and although Athletic threatened on more than one occasion, Barca held their advantage going into the break.
Yamal doubled the lead seven minutes into the second half and while Bilbao twice had the ball in the net in the closing stages, they were denied by offside decisions.
In their third successive final, Barcelona will face the winners of Thursday's semi-final between Real Madrid and Mallorca in the final on Sunday.Â
