On January 26, 2020, Altobelli died when a helicopter he was travelling in crashed in Calabasas. The pilot and the other seven passengers on board, among whom were Altobelli's wife Keri, their daughter Alyssa, Kobe Bryant, and the latter's 13-year-old daughter Gianna, were also killed. Alyssa Altobelli and Gianna Bryant were both members of the Mamba Sports Academy basketball team, and the group was reportedly on their way to a basketball game at the academy in Thousand Oaks when the helicopter crashed.

The day after the deaths of John, Keri and Alyssa, the Rochester Red Wings issued a statement to clear up confusion that despite similar last names, that John was not related to Joe Altobelli. The Red Wings closed their statement by offering their condolences to the families that lost loved ones in the crash.