Gaya was substituted in the 75th minute of the 4-0 win over Georgia on Sunday because of a muscle injury.
Among those missing were four players who also played with Spain in the Tokyo Olympics - Pedri González, Pau Torres, Mikel Oyarzabal and Dani Olmo.
In keeping with his tournament, Juventus striker Alvaro Morata was both hero and villain.
A crowd of 60,000 will be permitted for both semi-finals and the final at the home of English football as coronavirus restrictions are eased.
This might be a match between teams who have almost forgotten what it feels like to lose -Spain has only one defeat in its last 29 games — but Italy looks to have the edge, at both ends of the field.
Without Ramos, or any other Real Madrid player for the first time in Spain's history at a major tournament, the Madrid press cried foul, claiming La Furia Roja would lack leadership.
Spain coach Luis Enrique praised goalkeeper Unai Simon for the way he reacted to his mistake in the round of 16 match against Croatia.
All eyes will be on Croatia's Luka Modric for his goal-scoring and Spanish Striker Alvaro Morata for the lack of it.
Morata is under pressure after missing a golden chance against the Swedes, whose 1-0 victory over Slovakia on Friday means all four teams in Group E are still in the mix to reach the last 16.
Morata wasn’t the only one missing chances against Sweden, but he was the one being singled out by Spanish fans and media.
Spain captain Sergio Busquets is still self-isolating at home while defender Diego Llorente was only allowed to rejoin the group on Saturday after giving a fourth consecutive negative test.
Sergio Busquets left the team's pre-Euro 2020 training camp on Sunday, while the rest of the squad tested negative after their friendly draw with Portugal in Madrid at the weekend.
Luis Enrique is looking forward rather than to the past for inspiration as he controversially left out Sergio Ramos due to his fitness problems.
The major concern in Spain’s defense. Ramos, one of the main holdovers from the title-winning days, took the team’s penalty kicks and provided on-field leadership.
Captain Sergio Ramos, the 35-year-old Real Madrid captain has struggled with injury this season and has featured just five times since the start of the year.