The RFEF's executive committee met on Monday and unanimously approved Luis Enrique's appointment just eight days after the national team, under caretaker manager Fernando Hierro, were eliminated on penalties by hosts Russian Federation in the second round of the World Cup.
Hierro took over from Julen Lopetegui on a temporary basis, two days before Spain's first World Cup game.However The 2010 World Cup winners were knocked out of this year's tournament in the Round of 16.
Hierro stepped down from his post as caretaker boss on Sunday after Spain's early elimination from the World Cup - losing to hosts Russian Federation on penalties in the last-16. Spain left the tournament after winning just one game.
It emerged on Sunday that Rubiales was to put forward Lopetegui's successor to the RFEF's board on Monday and, shortly after doing so, Luis Enrique's appointment was made official.
The former Barcelona manager has signed a two-year contract to take charge of his country.
He also coached Celta Vigo and Barca's reserve team and has spent the past year on sabbatical since leaving the Nou Camp in May 2017.
The former Barcelona boss will lead La Roja into a new era after the hugely disappointing World Cup campaign.
"The last Spain coach has declined to return to his old job as sporting director of the Federation in order to look for new horizons and new professional challenges".
With Spain, Enrique will be aided by Jose Francisco Molina, 47, a former goalkeeper at Atletico Madrid and Deportivo La Coruna who played nine times for Spain and was named as sporting director.