But the jurors became deadlocked on a separate charge of involuntary manslaughter against Schwartz, prompting the judge to declare a mistrial.
The decision means prosecutors could seek another trial on the manslaughter charges in the death of Mr Elena Rodriguez, was fatally shot as he threw rocks at authorities during a drug smuggling attempt.
Late on 10 October, 2012, Schwartz fired 16 rounds in 34 seconds from three different firing positions, shooting through a 20ft fence which sits on an embankment above Mexico’s Calle Internacional, a Nogales street lined with homes and small businesses.
After emptying one magazine from his pistol, he reloaded and fired three more shots.
Prosecutors acknowledged Mr Elena Rodriguez was throwing rocks across the border, but said he did not deserve to die.
The defence countered that Schwartz was justified in using lethal force against rock-throwers and shot from the US side of the border in self-defence.
The judge told the jury in his instructions they could consider a lesser charge of voluntary or involuntary manslaughter if they had trouble reaching a verdict on the more serious charge.
During closing arguments, assistant US attorney Wallace Heath Kleindienst said Swartz “was fed up with being rocked” after being targeted in at least six other attacks.
“He was angry with those people who had been throwing rocks against the fence,” Mr Kleindienst said. “It was not about eliminating a threat, because there was no threat,” he said.
“It was about eliminating a human being.”
Defence attorney Sean Chapman argued there was “not a scintilla of evidence” Swartz was angry or fed up. He said Swartz shot because he was trying to protect himself and his fellow agents during a drug operation.
“From his first day in the Border Patrol, it had been ingrained in him that rocks were dangerous,” Mr Chapman said.
The trial played out as Donald Trump called for National Guard troops to be sent to the Mexican border to free up Border Patrol agents to concentrate on stopping drugs and people from illegally entering the US.
The US president has made his crackdown on illegal immigration and building a wall along the US-Mexico border a cornerstone policy of his presidency.
Additional reporting by agencies
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