Rubiales said Robert Moreno, the former assistant coach who steered Spain to Euro 2020 qualification after Luis Enrique left, wanted to stand down so that he could return.
Luis Enrique's daughter Xana passed away in September.
"Today we can confirm that Luis Enrique returns to his role as coach," Rubiales told a news conference.
Everyone knew that if Luis Enrique wanted to return he would have the doors to the national team open to him.
Moreno, who led the team to seven victories and two draws as Spain comfortably qualified for next summer's tournament, had said when appointed that he would step aside if Enrique wanted to return.