The boy was thrown overboard when a boat driven by his father hit a wave while they were sailing in open waters near Angel Island, north of San Francisco.
Javier A Burillo, 57, was arrested at his multimillion-dollar home in Belvedere on suspicion of vehicular manslaughter with a vessel, wilful harm or injury to a child, and operating a boat while under the influence.
Burillo and his two sons, aged 11 and 27, were the only people on board the 10m (33ft) Protector boat at the time.
Both sons fell off the vessel, although the older sibling escaped with cuts to his leg.
Burillo pulled the 27-year-old aboard first and the two men then rescued the younger son from the water, according to the Marin Independent Journal.
The paper also reported the boy had been struck by the boat as he was pulled from the water.
The father drove to the yacht club docks, where the 11-year-old boy was pronounced dead.
Tiburon police chief Michael Cronin said Burillo called authorities at 7pm, saying his son was injured and unconscious.
Online jail records show Burillo was released on $1m (£806,155) bail.
Burillo, whose full name is Javier Burillo Azcarraga, is a member of one of Mexico’s wealthiest families and is known for owning lavish hotels and restaurants in the country.
The Azcarraga family founded Grupo Televisa SA, which produces Spanish-language television programming across Latin America and dominates news coverage in Mexico.