Hermoso pressed charges against ousted Spanish Federation (RFEF) president Luis Rubiales earlier this month for his unsolicited kiss after the Women's World Cup final win over England in Sydney.
Tomé, who has replaced the sacked Jorge Vilda, said the decision was taken to "protect" the forward, who is now back in Mexico with her club side, CF Pachuca.
"We are with Jenni as we are with all the players," Tomé said Friday. "As for Jenni, we felt the best way to protect her in this squad was [by not picking her this time]."
Tomé has named 15 of the 23 players who helped Spain win the World Cup in her first squad, including back-to-back Ballon d'Or winner Alexia Putellas and UEFA Women's Player of the Year Aitana Bonmatí.
However, it remains unclear whether everyone called up has agreed to return to action for their country after 39 players -- including 20 in Tomé's squad -- released a statement on Friday seeking changes at the RFEF beyond Rubiales' resignation and Vilda's dismissal.
"I have confidence that all the players are professionals," Tomé limited herself to saying when pressed on whether the call-ups were consensual.
"They are on the back of becoming world champions. They love this profession. It is a privilege to be part of the national team."
Spain face Sweden in Gothenburg on Friday and then host Switzerland in Cordoba on Tuesday, Sept. 26. Both games are in the Nations League, which also serves as the qualification pathway for next summer's Olympics.
The situation dates back to last September, when 15 players announced they were not available for selection until changes were made at the RFEF, but things have accelerated since Rubiales' behaviour after the World Cup final.
Rubiales planted an unsolicited kiss on forward Hermoso's lips, also grabbing his crotch, hugging and kissing other players, and throwing Athenea del Castillo over his shoulder after Spain's win.
He is facing charges of sexual assault and coercion for the kiss on Hermoso, who pressed charges earlier this month. The coercion charges relate to the pressure he is accused of putting on Hermoso and her relatives to say that she justified and approved what happened.
In August, 81 current and retired internationals said they would not play for Spain again under the current leadership and, on Friday when the squad was due to be announced, 39 said sufficient changes had still not been made.
The players called for a restructuring of women's football within the RFEF, as well as changes to the president's cabinet, the media and communications department, and the integrity department.
Earlier on Monday, before the squad was announced, the RFEF released a statement saying they "urge the players to join the changes" they promised to enact across the federation.
None of the players have positioned themselves since Friday.
According to Spanish sports law, athletes are required to answer the call of its national teams unless there are circumstances that impede them from playing, such as an injury. Should they refuse the call, the players face sanctions including fines of up €30,000 ($32,000) and the suspension of their federation licence for two to 15 years.
Also on Monday, a Spanish court dismissed a lawsuit by Rubiales against coach Javier Clemente, who had called Rubiales a "dangerous and ambitious guy" seeking "to get rich," qualifying his comments as free speech.