Cox was accused of sexually assaulting a woman at his apartment in September 2010 after a night of partying. She became pregnant, and prosecutors said DNA tests indicated Cox was the father.
Cox hugged his attorney after the verdict was read, while the alleged victim let out an audible sigh and a cry. As she was leaving the courtroom, she said, "Oh my God, what's happening?"
Cox expressed appreciation for his attorney, Harvey Steinberg, and others who supported him during the trial.
"I love my lawyer and everybody else who's been," with me, he said.
Steinberg had disputed the DNA test results and suggested they may have been contaminated. During the cross-examination of witnesses, he tried to paint a picture of drunkenness and of the alleged victim being able to interact with people without remembering.
"We always felt there were substantial holes in the case," he said after the verdict. "We had hoped they (the jury) would see those same holes."
Jurors left the courthouse without commenting.
Cox denied having sex with the woman, who testified that she believed she was drugged because she remembers little about what happened.
Cox was charged with one count of sexual assault while the victim was physically helpless and one count of sexual assault while the victim was incapable of determining the nature of the conduct. He faced two years to life in prison if convicted.
Prosecutors had laid out what they believed was a straightforward case. They cited the DNA evidence, as well as testimony from Cox's teammate, Demaryius Thomas, who said he saw Cox carry her onto his bed and say, "she's ready."
Prosecutor Chris Gallo said Cox's statement showed what state of mind he was in. Gallo told jurors that Cox expected to have sex with another woman at the apartment, Carthy Che, who testified she was sick. And there was the alleged victim, lying on his bed and "ready."
Jurors heard from the alleged victim on Wednesday. Cox did not testify, but jurors on Friday saw a portion of an interview with detectives conducted the night he was arrested.
In the video, Lone Tree Police Department Detective Steve Hipp informs Cox that his DNA indicates he impregnated the woman. Cox then sits back and says, "Are you serious?"
"I never raped nobody," Cox told the detective as both spoke in loud voices. "I'm losing it because, seriously, I never touched this girl."
The interview ends with Cox asking: "I'm going to jail? You're kidding me. What am I supposed to do? I didn't."
Cox also told the detectives that Che, who he was dating at the time, was also at the apartment. He said he could have had sex with her if he wanted sex.
Cox, 25, was a rookie out of Oklahoma State who had played eight games for the Broncos when he was arrested.
His legal troubles capped a tumultuous time for the Broncos, who had dealt with the drive-by slaying of cornerback Darrent Williams on New Year's Day 2007, running back Damien Nash's fatal heart attack in March 2007 and receiver Kenny McKinley's suicide in September 2010.
Prosecutors said they wouldn't immediately comment on the verdict. The accuser's attorney, Craig Silverman, didn't respond to a request for comment.
Steinberg said he realized the trial was a terrible ordeal for the woman.
"We know this has been a very difficult situation for her," he said. "It's been a very difficult situation for Mr. Cox. We're thankful that it's over."