Gentile is the daughter of Laura Bonafede, a teacher who was in a relationship with Messina Denaro for many years.
The mobster is said to have considered Gentile a daughter and she is thought to hold many of his secrets.
A judge had previously turned down a request from prosecutors for Gentile to be held in jail on remand.
But on Tuesday a court granted a petition for her to be put under house arrest on the basis of new material presented by the Carabinieri. Messina Denaro died in a hospital in L’Aquila in September aged 62 after a battle with cancer.
The last godfather of the Sicilian mafia’s long spell on the run ended when he was caught in a Palermo cancer clinic on January 16.
Messina Denaro had been convicted for his involvement in dozens of murders, including the 1992 Cosa Nostra bombings that killed anti-Mafia magistrates Giovanni Falcone and Paolo Borsellino.
In addition to the Falcone and Borsellino assassinations, he was condemned for the killing of Giuseppe Di Matteo, the 12-year-old son of a mobster-turned-State witness who was strangled and dissolved in acid in 1996, and bombings at art and religious sites in Milan, Florence and Rome that killed ten people and hurt 40 more in 1993.
ANSA