Wide receivers Kendall Sanders and Montrel Meander were in custody at the university police station. According to an arrest affidavit, Sanders and Meander texted each other during earlier interviews with police to "get their story straight," and Sanders also faces a charge of improper photography tied to the alleged assault on June 21.
First-year Longhorns coach Charlie Strong, who will welcome his team to preseason training camp in two weeks, said he has suspended both players.
"We've been monitoring and addressing the situation with Kendall and Montrel since it was brought to our attention," Strong said in a statement released by the school. "It's been made clear to everyone on our team that treating women with respect is one of our core values, and I'm extremely disappointed that two young men in our program have been accused of not doing that."
The sexual assault charges carry prison terms of two to 20 years.
"It's a shame that a mere allegation can affect a young man's life to the extent this will," said Sanders' attorney, Brian Roark. "Kendall Sanders is innocent, though, and eventually, that will be proven."
According to arrest affidavits, the alleged victim knew both men for more than a year.
Police said they were called to her dorm at 3:43 a.m. and found the woman under an entryway service desk, crying, barefoot and disheveled. The woman told police she had gone to Austin's Sixth Street entertainment district with friends and agreed to return to Meander's dorm, where they began to have consensual sex.
Sanders then knocked on the door, and Meander let him in, according to police. The woman said Meander went into the bathroom and that Sanders forced her to have vaginal and anal sex.
Meander returned and joined the assault despite her telling both of them to stop, according to police. She told police that she also suspected that Sanders used his mobile phone to take a picture or video of her.
Detectives separately interviewed both players at the university police station. Police said the players agreed to let police look at pictures on their phones, and detectives said they found at least one photo of the victim.
"The university campus must be an environment free from all sexual assault and violence," Texas president Bill Powers said in a statement released Thursday. "At the University of Texas at Austin, student safety is our top priority and we are involved with the national efforts to prevent a culture of sexual violence from taking root on campuses. We educate all of our students about preventing sexual assault and vigorously investigate all allegations so we can take the appropriate action."
Sanders, a junior, has played in 23 career games and started seven last year. He has 39 career receptions for 376 yards and one touchdown. Sanders was suspended for the 2013 season opener after a drunken-driving arrest. Meander is a redshirt freshman who did not play last season.
Powers' statement said the allegations have been and will continue to be thoroughly investigated and that the university has undertaken an internal student judicial review.
"I commend [UT police] Chief Carter for conducting a fair and thorough investigation and Coach Strong for making a decision that is in the best interest of his team and the university," Powers said. "We encourage everyone to respect both the criminal and administrative review processes as they continue."
ESPN.com's Max Olson and The Associated Press contributed to this report.