Cox is accused of sexually assaulting the woman, who testified earlier Wednesday. Both the woman and Thomas told jurors they kissed on an air mattress at Cox's apartment after meeting up at a club with Cox and Cox's girlfriend.
Thomas said the woman fell asleep, and he dismissed Cox's suggestion, saying he didn't want to have sex with the woman because she was drunk.
"I wanted to have sex with her but I didn't," Thomas testified. "We hadn't done nothing before. I wasn't going to try nothing that night because she had been drinking. She had got drunk."
Thomas testified that Cox then sat with him in the living room for a while. He said the woman was still in the bedroom when he left about an hour later.
The woman testified that she had a fuzzy memory of what happened that night and suspected she had been drugged after she woke up feeling sick the next day.
Under questioning from Cox's attorney, the woman said if something had happened with Thomas, she wouldn't have considered it rape.
"It wouldn't have been fine but I wouldn't have seen it as rape if he admitted it," she said, referring to Thomas.
She said Thomas denied that anything had happened. Later, she found out she was pregnant and contacted authorities on Oct. 28, 2010. Investigators say DNA tests indicate Cox is the father.
Thomas and Vaughn also submitted DNA samples and were cleared.
The Associated Press isn't identifying the woman because she's an alleged victim of a sexual crime.
Cox has pleaded not guilty to 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 faces two years to life in prison if convicted.
A witness list of those who are expected to testify in Castle Rock, 30 miles south of Denver, remains sealed although Douglas County District Court Judge Paul King told potential jurors two other Broncos - linebacker Wesley Woodyard, and special teams specialist Cassius Vaughn - could be also be called.
Vaughn was Cox's roommate at the time who said he was asleep in the apartment that night.