Bubaris closed his eyes as the forewoman began reading the verdict, then bit his lip as the second "not guilty" was pronounced. Muted cries of "Yes!" and a few sobs came from his family and friends in the gallery.
Bubaris, 31, could have faced up to 15 years in prison if convicted.
Outside court, jurors noted a lack of forensic evidence and conflicting medical testimony in the case.
No bias crime was alleged, and no clear motive was offered, but the case brought attention to the sometimes tense relationship between officers and immigrants as police departments nationwide consider whether to take on increased deportation duties. The advocacy organization Hispanics Across America said the case also spotlighted the helplessness of many illegal immigrants.
The group's president, Fernando Mateo, called the verdict a travesty.
"This is exactly what we were afraid of. ... Apparently the rights that we hold so dear as Americans did not apply to Rene Perez and to Hispanics in general," Mateo said.
He called for a federal prosecution, and U.S. Attorney Michael Garcia said federal agents could still pursue the case.
"We will undertake an independent review of all of the available evidence to determine whether any federal criminal civil rights laws have been violated," he said.
Perez's brother, Anival Perez, was in the courtroom but would not comment. A friend, Mauricio Arriga, said the family remains convinced that Bubaris "had something to do with this killing."
Perez, 42, left a wife and child in Guatemala when he came to Mount Kisco a decade ago. He became well known to police as a vagrant, a drunk and a frequent 911 caller.
Prosecutors claimed Bubaris took Perez to neighboring Bedford in his patrol car and killed him with a punch to the abdomen soon after Perez called 911 from a Mount Kisco coin laundry on April 28, 2007. The defense said the chronically intoxicated Perez could have been hurt just by falling on something.
Jurors heard a fellow officer testify that Bubaris told him - on the night Perez died - that he'd gone out "hunting" or "looking" for the immigrant. And when word of the death spread, the officer testified, Bubaris told him, "You're the only one that knows, bro."
The officer acknowledged on cross-examination, however, that he didn't tell anyone about those statements until he had been granted immunity.
Medical experts voiced conflicting views on when Perez's injury - a tear in the mesentery, which carries blood to the intestines - could have happened. Prosecution witnesses insisted it had to have occurred within the last few hours of Perez's life, after Bubaris responded to the 911 call, because the injury would have severely disabled Perez. Defense witnesses said the wound could have been much older.
Jurors found the medical evidence too inconclusive.
"What caused the injury is very speculative," said Richard Hodder of Hawthorne. "We just could not come to the conclusion that the officer did something to injure him."
Geoff Haynes of Croton-on-Hudson noted there was no DNA or other forensic evidence linking Perez to Bubaris or his patrol car.
"Without that, it was really difficult for us to send Mr.
Bubaris to prison," he said.
District Attorney Janet DiFiore issued a statement saying, "We accept and respect the jury's verdict."
Bubaris did not speak to reporters as he left the courthouse.
Defense attorney Andrew Quinn said Bubaris spent the first 15 minutes after the verdict "just hugging his wife."
He said Bubaris, who resigned from the police force after he was charged, had not talked about what he would do now. It's difficult to plan, he said, "when you're looking at the possibility of 15 years in state prison."
