Roma Women captain Elisa Bartoli was the player to break the deadlock in the game on the island, as she wriggled into space inside the box before firing home.
A late penalty from Juventus forward Cristiana Girelli, won by Roma's Manuela Giugliano, confirmed the victory.
Roma due Annamaria Serturini and Giada Greggi both sat on the bench throughout the game.
On the other side, former Roma defender Emma Lipman made her international debut for Malta in the game.
It was Bartoli's second goal in three qualifying games, as the Azzurre now prepare to face Bosnia & Herzegovina in Palermo next week.
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