Archbishop George Lucas, who served in Springfield from 1999 to 2009, was a priest and the dean of education at the St. Louis Preparatory Seminary School in the late 1980s when the alleged abuse occurred.
The 75-year-old Lucas has led Archdiocese of Omaha since leaving Springfield.
Lucas' male accuser, only identified by the initials "D.S." in the petition, was a 16-year-old high school junior at the time.
According to the filing, Lucas performed oral sex on the student and masturbated while performing the act, mostly during "one-on-one check-in sessions." The student was enrolled in two courses Lucas taught.
On multiple other occasions, Lucas masturbated the student and forced him to masturbate Lucas, according to the lawsuit.
When Lucas failed the student on an assignment, he told the student he could perform oral sex for a better grade.
"D.S." said he saw another unnamed student performing oral sex on Lucas.
Lucas, a native of St. Louis, later served as the archdiocese's chancellor and then rector of Kenrick-Glennon Seminary.
It was Lucas who called for an independent investigation of the Springfield diocese led by Bill Roberts, a former federal attorney.
Roberts' 2006 report stated in part that Lucas' predecessor, Bishop Daniel L. Ryan, fostered "a culture of secrecy" in the diocese that discouraged priests from coming forward with information about sexual misconduct by other priests. It also said Ryan, who served as Springfield bishop from 1984 to 1999, "engaged in sexual misconduct with adults and used his authority to conceal this misconduct."
Ryan died in 2015.
The report led to the removal of eight priests from around the 28-county diocese.
One of the groups, Survivors Network of those Abused by Priests (SNAP), that said the 2006 report didn't go far enough had strong reaction to the lawsuit.
"We firmly believe Lucas hid clergy sex crimes while he was in Springfield," said David Clohessy, the former national director of SNAP from St. Louis. "He may well have committed such crimes, too. We hope every single person who might shed light on these allegations, especially current and former church employees, will do their civic and Christian duty by coming forward now and speaking up."
Through a spokesperson, Lucas on Thursday said: "I categorically deny the accusation made by an anonymous person. I have never had sexual contact with another person. I referred the matter to (Cardinal Christophe Pierre), Pope Francis' representative in Washington, D.C., for his guidance."
The St. Louis archdiocese, the petition claimed, "knowingly enabled, covered up, and concealed that for multiple decades their employees sexually abused minors."
It labeled the cover-up as "shameless."
The lawsuit naming Lucas was filed in St. Louis County Circuit Court.