Other former marines testified during the five-day trial that they heard gunshots but did not see Nazario kill the detainees.
Thursday's verdict marks the first time a civilian jury has determined whether the actions of a former soldier in combat violated the law of war.
"It's been a long, hard year for my family," Nazario said outside the courtroom.
"I need a moment to catch my breath and try to get my life back together."
Ingrid Wicken, the jury forewoman, said the panel acquitted Nazario because of insufficient evidence.
"I think you don't know what goes on in combat until you are in combat," she said.
The former marine's lawyer, Kevin McDermott, said he believed the verdict would curb faulty legal filings.
"I don't think they are going to put on a case in the future with a lack of evidence."