The former Lanus and Palermo trainer takes over at the Bombonera alongside twin Gustavo, having enjoyed a stellar career with the Xeneize as a player.
Former Boca Juniors forward Guillermo Barros Schelotto has been named the club's new coach after Rodolfo Arruabarrena paid the price for a disappointing start to the club's title defense.
Boca has won just two of five Primera Division games this term under Arruabarrena, having lifting the domestic title and the Copa Argentina last season.
Sunday's 1-0 defeat to Racing Club proved the final game of his two-year tenure, as he left a day later, with Barros Schelotto - hugely popular among fans at La Bombonera - holding his first news conference as coach on Wednesday.