Arizona released a statement saying Miller and the school agreed to the decision, citing the "best interests of the University and the basketball program."
Miller issued a statement echoing the school's sentiment while saying he is "confident that I will be vindicated."
"I believe it is in the best interest of our team that I not coach the game tonight," Miller said in the statement. "I continue to fully support the University's efforts to fully investigate this matter and am confident that I will be vindicated. For now, my thoughts are with our team. They are a great group of young men that will support each other and continue their pursuit of winning a Pac-12 championship."
ESPN reported Friday that FBI wiretaps intercepted phone conversations between Miller and Christian Dawkins, an employee for ASM Sports agent Andy Miller. According to sources familiar with the government's evidence, Sean Miller and Dawkins discussed paying $100,000 to ensure that Ayton would sign with the Wildcats.
Prior to Saturday's game, a lawyer representing Ayton's family released a statement saying they were "outraged and disgusted by reported recent news stories which have falsely implied" their involvement.
"[Ayton] directly stated to the FBI, more than six months ago, that he never discussed or solicited payments from the University of Arizona, or any other university, or any shoe company or anyone on behalf of either -- Period. This includes basketball and anything else," the statement said.
Asked earlier Saturday about ESPN's report on Arizona, NCAA president Mark Emmert said it is up to the school to decide whether to hold out Miller or Ayton.
"First and foremost, that's a decision the school has to make," Emmert said in an interview on CBS.
Emmert noted that no NCAA process has been initiated into Arizona.
Asked whether the NCAA has been in touch with Arizona, Emmert said, "We've been in touch with every school that has a student-athlete involved [in the FBI investigation into the sport]."
The Arizona board of regents met in an emergency executive session Saturday "to receive legal advice regarding the issue and plans to reconvene for updates and legal advice in the coming days."
"This is an emotionally charged issue but it is essential that we move forward decisively and based on facts," regents chair Bill Ridenour said in a statement. "We must do everything we can to ensure that our programs are of the highest caliber as we must also protect the rights of all involved and respect due process for employees."
Miller and Dawkins had multiple conversations about Ayton, sources told ESPN. When Dawkins asked Miller if he should work with assistant coach Emanuel "Book" Richardson to finalize their agreement, Miller told Dawkins he should deal directly with him when it came to money, the sources said.
The telephone calls between Miller and Dawkins were among 3,000 hours of conversations intercepted from Dawkins' phone by the FBI.
Ayton, a 7-foot-1 center who was born in the Bahamas, is considered one of the top freshmen in the country and a leading candidate for national player of the year honors. He is averaging 19.9 points and 11.2 rebounds per game in what is expected to be his only college season.
Richardson, who worked for Miller the previous 10 seasons at Xavier and Arizona, was one of four assistant coaches arrested by FBI agents on Sept. 27 after a two-year investigation into bribes and other corruption in the sport.
Richardson is accused of accepting $20,000 in bribes and paying a recruit to sign with the Wildcats. In exchange for the money, the government alleges, Richardson agreed to influence Arizona players to sign with Dawkins and financial adviser Munish Sood, who also was arrested by FBI agents.
Arizona formally fired Richardson on Jan. 11.