Guardiola's contract ends at the close of the season and the former player rejected Barcelona's offer to extend his deal. His last game in charge will be the Copa del Rey final against Athletic Bilbao on May 25.
"The reason is simple, four years are long and they wear you down," Guardiola said Friday after president Sandro Rosell announced he would not continue. "I think that sincerely that the next person will have things to bring that can't.
"Every day during four years, the demands are very high, the pressure, the necessary energy to push the players and enjoy it. I need to rest and move away."
Rosell said Vilanova, who has served as Guardiola's assistant since he was promoted from B-team manager, would take over the coaching duties.
The 41-year-old coach has led Barcelona to 13 trophies since replacing Frank Rijkaard at the beginning of the 2008-09 season, including two Champions League crowns and three Spanish league titles.
Guardiola's decision ends a difficult week for the team that saw it exit the Champions League semifinals to Chelsea following a loss to Real Madrid which will likely cost it a fourth straight Spanish title.