Fernando Hierro, Spain's director of football at the time, stepped in to take the reins over the course of the tournament, as La Roja were eliminated in the last 16 by Russian Federation in a penalty shoot-out after a 1-1 draw.
Hierro, 50, has chose to "seek new horizons", according to the Spanish football federation (RFEF).
A team with a history of success, a talented squad and a distinctive style of playing, had just failed to win a trophy for the first time in six years.
His appointment was announced this afternoon at a press conference by president of the Spanish Football Federation, Luis Rubiales.
Of the starting XI against Russian Federation, only Marco Asensio will be under 30 when the next World Cup comes around.
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It killed six civilians on Thursday, including a woman and four children, according to the Britain-based Observatory. Government forces in south Syria have advanced along the Jordanian border, seizing a string of villages.
Lopetegui had taken the Real Madrid job without informing his employers, a betrayal that left Rubiales and the Spanish FA seething.
He previously coached Celta Vigo and Barca's reserves, as well as Serie A side Roma.
The 48-year-old has been out of work since leaving Barcelona last summer.
Spain, who won back-to-back European titles (2008, 2012) and the 2010 World Cup, are hoping to open a new successful chapter under Luis Enrique after three consecutive disappointing tournaments.
Molina, 47, is a former Spanish national goalkeeper and also played for Atletico Madrid and Deportivo de la Coruna.