Paterno released a statement today saying he was "absolutely devastated" by the scandal and would retire at the end of the season.
ABC News has learned that Spanier will be ousted from his position today, according to Penn State sources.
The turmoil follows the arrest of former assistant coach Jerry Sandusky, charged with abusing at least eight boys over 15 years.
Athletic director Tim Curly and Vice President for Finance Gary Shultz were charged Tuesday with not reporting the sexual abuse to police and lying to a grand jury under oath during the investigation.
Paterno and Spanier have come under intense pressure this because they were also told of at least one incident, but did not alert police.
"I am absolutely devastated by the developments in this case," Paterno, 84, said in a statement today. "I grieve for the children and their families, and I pray for their comfort and relief."
"This is a tragedy. It is one of the great sorrows of my life. With the benefit of hindsight, I wish I had done more," he said.
Paterno, who has coached the team for 46 years and is the winningest coach in top level college football ever, said it has been his intention to "serve the best interests of this university and the young men who have been entrusted to my care."
"That's why I have decided to announce my retirement effective at the end of this season. At this moment the Board of Trustees should not spend a single minute discussing my status. They have far more important matters to address. I want to make this as easy for them as I possibly can," Paterno said.
The coach had a closed meeting with his team and coaching staff this morning where he reportedly broke down in tears while telling them he was leaving, according to the Associated Press. Players, also choking back tears, gave him a standing ovation as he walked out of the gym, the report said.
Penn State representatives did not have an immediate comment.
Paterno was showered with affection by Penn State students who showed up outside his house Tuesday night.
"I've lived for this place. I've lived for people like you guys and girls," Paterno said when he emerged from his home. "It's hard for me to say how much this means.
"As you know, the kids that were the victims. I think we ought to say a prayer for them," he said.
Sandusky was arrested Saturday and charged with molesting eight boys over 15 years, all of whom he met through his charitable organization, The Second Mile, a group home and outreach program for troubled boys.
The charges stem from a March 2002, incident in which graduate assistant coach Mike McQueary allegedly saw Sandusky sexually assaulting a boy in a locker room shower in the Penn State football department. McQueary told Paterno what he saw, and Paterno in turn told Curly and Shultz. None of the men reported the incident to police.
The Pennsylvania attorney general said Monday that Curly and Shultz were legally required to alert police to the incident, while Paterno was only legally obligated to tell his superiors. But Paterno has come under fire for failing what police called a "moral obligation" to alert them to the crimes.
Pressure has also increased on Spanier because Curly and Shultz reported to Spanier that there had been an inappropriate incident with Sandusky and a child in the locker room showers, and that they had taken away Sandusky's privilege of bringing children onto campus. Spanier approved the decision and never reported the Sandusky incident to police.
Sandusky allegedly molested some of the children that he brought to the Penn State campus to meet the team members and work out at the facilities. He also brought them along on trips to away games and plied them with gifts, according to the presentment.
Two earlier sexual assaults on campus had been brought to the attention of employees and administrators, neither of which were reported to the police, according to the attorney general. In 1998 two boys reportedly came forward to say Sandusky had fondled them in the team's showers. Campus police had eavesdropped on a conversation between Sandusky and one boy's mother. That mother recently described the exchange to local reporter Sara Ganim with the Patriot News.
"He admitted to taking the shower, he admitted to some extent something bad happened," the woman, who was not identified, said. "He asked her for forgiveness. He said 'I probably won't get it from you,' and then he said 'I wish I were dead.'"
The mother said that she was proud of her son, who had the courage stand up to one of the giants of college football, according to Ganim. The boy's allegation led to the three-year grand jury investigation that resulted in sexual assault charges.
Sandusky was a coach and defensive coordinator for the team for 23 years before retiring in 1999. After his retirement, he continued to have unlimited access to the football department and campus, and continued to run football camps for boys at Penn State's campuses.
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