Actors Naomi Watts and Matt Dillon made the announcement before 5,000 attendees at the event, part of the two-week long Tribeca Film festival.
The film focuses on a girl who tries to prevent her father from spiraling into depression and alcoholism after her mother's death. Bonifacio's prize package included $2,500 and Final Cut Pro software from Apple.
"Daily Show" fake news correspondent Ed Helms hosted the evening. And a panel of judges, including director Darren Aronofsky, producer Caroline Baron, actress Famke Janssen, actor Anthony Lapaglia, and screen writer Charles Randolph, picked Bonifacio's film as winner.
"The turnout tonight at the first Tropfest@Tribeca exceeded my expectations," said John Polson, a director and founder of the event in a statement. "I think everyone had a fantastic time watching the work of these eight filmmakers with the Hudson River in the background. It couldn't have been any better."
Bonifacio beat out seven other short films, all of which were under seven minutes in length and featured a manhole cover somewhere in the film as a Tropfest "signature" item.
The event was modeled after the original Tropfest, an Australian short film festival established in the 1990s that is still the country's largest. The competition, supported by Australia's most prominent film personalities, illustrates the importance of short films.