Fernando Hierro, who led Spain at the 2018 World Cup, has stepped down as coach and will not return to his former role as sporting director.
Hierro, 50, has decided to “seek new horizons”, according to the Spanish football federation (RFEF).
A statement said the former Real Madrid player had “declined” to return to his previous role and has opted to “undertake new professional challenges”.
Lopetegui was sacked two days before their opening World Cup match with Portugal after he was named Real Madrid boss.
Lopetegui became Spain manager in 2016 following Vicente del Bosque’s retirement, and remained unbeaten through his reign.
After their surprise exit to Russia, Hierro said he accepted responsibility for the team’s failure to advance any further.
“We all tried to give it our best but that’s football,” he said.
“I don’t think you can talk about the team breaking down or collapsing. There’s a fine line between winning and losing.”