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.
The woman's attorney, Craig Silverman, said she still believes she did the right thing by going to police, and she doesn't want other sexual assault victims to be discouraged from coming forward.
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.
Prosecutors never explained whether they determined if the woman had been drugged, saying that wasn't necessary to proving the case. Steinberg, however, argued that she may have been an experienced drinker, admitting on the witnesses stand to having 21 drinks on her 21st birthday, and that she was drunk at the time but able to walk and talk to people without remembering.
While the woman only remembers passing out on the air mattress in Cox's living room, Cox's teammate and roommate who was at the apartment that early morning, Cassius Vaughn, told Thomas that the woman had sex with Che that morning, according to testimony.
Steinberg raised the question to the jury, that if she didn't remember walking away from a nightclub and talking to people two blocks away, which she said she did on the witness stand, or climb up three flights of stairs on her own, then she may not have remembered having sex that night.
Steinberg criticized Deputy District Attorney Chris Gallo and Assistant District Attorney Bob Chappell for not calling Vaughn to the witness stand to explain his statement about "girl on girl action."
"Where is he? Steinberg asked the jury during closing arguments. "Are they afraid of the truth?"
Afterward, Gallo said he didn't believe Vaughn's testimony was essential to their case.
"There are certain things that we have to prove and we put on the evidence that we thought would prove" our case, he said. "What goes on in a jury room, for a very good reason, nobody really knows."
Vaughn did not return a message left by The Associated Press.
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.
Cox's agent, Jordan Woy, said he has spoken to several interested NFL teams.
"We expect for him to move forward in his NFL career," Woy told The Associated Press in an email. "Perrish is looking forward to focusing on his life both personally and professionally."
Associated Press Sports Writer Pat Graham contributed to this report.