Mr Netanyahu, along with Maharashtra Chief Minister Devendra Fadnavis, laid wreath at the memorial of the terror attack victims that claimed 166 lives, at the iconic Taj Mahal Palace Hotel in south Mumbai under a heavy security blanket.
The Israeli prime minister also wrote a message in the visitor's book at the place.
Mr Netanyahu later visited the nearby Nariman House, where he met 11-year-old Israeli boy Moshe Holtzberg.
Moshe's father Rabbi Gavriel Holtzberg and mother Rivka were killed at the Nariman House during the 2008 attacks.
The Jewish couple ran a cultural and outreach centre for the Chabad-Lubavitch movement at the Nariman House in south Mumbai's Colaba area.
Moshe came to Mumbai on Tuesday, returning to the place where he was orphaned nine years ago in the terror attack.