Vilda led Spain to the Women's World Cup title in the summer, when they defeated England 1-0 in the final.
However, the 42-year-old was sacked within a month amid the fallout from the Luis Rubiales scandal.
He replaces Reynald Pedros, who helped Morocco qualify for their first Women's World Cup in 2023 and guided them to the last 16, where they lost to France.
"The Royal Moroccan Football Federation contracted the Spanish coach Mr Vilda to coach the women's national football team in the next stage," the Moroccan football federation said in a statement.
It thanked Pedros for "the work he accomplished, especially the qualification to the second round of the World Cup".
Spain beat England in the World Cup final on 20 August but the win was overshadowed by Rubiales kissing forward Jenni Hermoso, which she has said was not consensual.
Vilda - considered a close ally of Rubiales - is being investigated as part of the criminal case against the former Spanish football federation (RFEF) president, who denies charges of sexual assault and coercion.
Spanish media have reported Vilda is being investigated for his part in the alleged coercion of Hermoso, who said pressure was put on her, her family and her friends to defend Rubiales' actions. Vilda has denied this.
Vilda, who was in charge of the Spanish national team from 2015, survived a player 'revolt' in September 2022, when the RFEF released a statement revealing 15 players had submitted identical emails saying they would not play for Vilda unless "significant" concerns over their "emotional state" and "health" were addressed.
'Las 15' - as the players became known - denied claims they had asked for Vilda to be sacked, but tension followed amid reports of concerns over training methods and inadequate game preparation.
