Superior Court Judge A. Leon Stanback, Jr. will take Cline's place pending a hearing to remove her from office.
"He is the ideal person to bring strong leadership to the district attorney's office at this challenging time," said Perdue in a statement.
Stanback was on the bench for 20 years. He served on the Parole Commission and was an assistant DA in Guilford County at one point.
Cline was suspended Friday by Franklin County Judge Robert Hobgood who ruled a petition against Cline by Durham lawyer Kerry Sutton has merit. He set a hearing date for Monday February 13.
Sutton's 11-page affidavit filed last month says Cline should be removed from her office on the grounds of habitual intemperance and conduct prejudicial to the administration of justice. In his filing, Sutton said ongoing attacks Cline has made against Superior Court Judge Orlando Hudson are grounds for her removal.
Cline has been feuding with Hudson for months and has accused him of bias against her in cases. Cline has even called the judge dishonest and corrupt - and asked that he be barred from hearing criminal cases in Durham County in a complaint to the Judicial Standards Commission.
The feud began when Hudson threw out the case against Derrick Allen, who had been in prison since he was convicted in the 1998 death of 2-year-old Adesha Sikia Artis. He spent more than 12 years behind bars after pleading guilty under pressure from family and lawyers to avoid the death penalty.
In his ruling, Hudson said prosecutors intentionally kept information from Allen that would have helped his defense.
Cline and Hudson butted heads again when he dismissed the case against Michael Dorman. He was charged with murder in the death of 31-year-old Lakeia Boxley - who disappeared from her Durham apartment in March 2008. Prosecutors said Dorman even carried Boxley's bones around with him in a backpack.
But before Dorman's defense attorneys had a chance to have independent testing done on the remains, they were cremated.
Hudson blasted Cline in his ruling - accusing her office of "flagrantly violating" Dorman's constitutional rights by destroying critical evidence and allowing inaccurate testimony during hearings focused on his case.
In a highly unusual filing, Cline fired back that her refusal to dismiss the charges in the Allen case "ignited a purposeful pattern of abuse of discretion and intentional misconduct" by Hudson.
Critics say Cline's actions against Hudson are undermining the integrity of the court.
In his ruling Friday, Judge Hobgood said he found no evidence of habitual intemperance, but found evidence of conduct prejudicial to the administration of justice.
"…the conduct and actions of Tracey E. Cline are prejudicial to the administration of justice which brings the office of the District Attorney into disrepute," he ruled.
Cline has not responded to interview requests for ABC11, but she has denied any wrongdoing in the past.
At the hearing later this month, Sutton will be allowed to call witnesses and Cline will be able to call witnesses and testify on her own behalf.
In the meantime, Cline will continue to draw her salary.