John Anthony Ruiz, 42, of Los Banos, is still in critical condition, police said Wednesday.
At about 10:20 a.m. Friday, Gilroy police responded to a report of suspicious activity at a restaurant in the area of Monterey and Howson streets.
Witnesses inside the business reported that a naked man was holding and shaking a baby and making nonsensical statements, police said.
Patrons managed to distract the man, later identified as Ruiz, and grab the baby, but he allegedly responded violently before some bystanders were able to hold him down until officers arrived, police said.
Ruiz then resisted arresting officers, who used pepper spray to try to subdue him but he continued to struggle, police said.
Almost immediately after a pair of officers managed to handcuff Ruiz, he stopped breathing and went into cardiac arrest, police said.
Emergency medical personnel, already at the scene, began treating Ruiz and transported him to the hospital, police said.
The baby was examined at a hospital and was uninjured, and was then released to the custody of the Santa Clara County Department of Family and Children's Services, police said.
Police detectives later determined that Ruiz was the father of the baby.
He had displayed signs of being under the influence of a drug and police recovered methamphetamine among his possessions, police said.
Ruiz had recently been released from the Santa Clara County Jail after being arrested for a parole violation, police said.
Police are seeking a warrant for Ruiz's arrest on suspicion of felony child endangerment, resisting arrest, possession of a controlled substance and being under the under the influence of a controlled substance, police said.
The Gilroy Police Department's internal affairs unit, Gilroy police detectives and the Santa Clara County District Attorney's Office are investigating why Ruiz suffered from medical distress during his arrest, police said.