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 later expressed his relief about the verdict on Twitter.
"The feeling i have right now can never b felt, cant b explained, the lord has his ways of work, glad i was able 2 b in the path of that!!" Cox wrote.
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.
He told the Denver Post Friday that intends to return to the league next season.
"Oh yeah, I've been working out every day," Cox said. "Through this whole process (playing again), that's what kept me grinding. I've been running, swimming, lifting weights every day."
Cox said that while some organizations have shown interest, he will not be playing for the Broncos, telling the newspaper that he thinks "it's best if I get a fresh start somewhere else."
The woman's attorney told The Associated Press Friday that the alleged victim still believes she did the right thing by going to police.
The attorney, Craig Silverman, said in a statement that she believes there was wrongdoing and dishonesty by Cox and his teammates. He says she doesn't want other sexual assault victims to be discouraged from coming forward.
The Associated Press contributed to this report.