In the ruling delivered on Friday, the court threw out a petition to have the DCJ removed, which had been filed by the Director of Public Prosecutions (DPP) and the Directorate of Criminal Investigations (DCI) before the Judicial Service Commission (JSC).
DPP and DCI had sought to have DCJ Mwilu removed over what was termed as gross misconduct.
Justice Said Chitembwe, Roselyn Aburili and Weldon Korir ordered that the DCI and DPP have no grounds for the petition.
They explained that allowing the law enforcement bodies to make such a petition would violate the separation of powers tenet of the laws of Kenya.
In May 2019, the same court had ordered to have all corruption cases against the DCJ be stopped.
A five-judge bench delivered the ruling stating that the manner in which DCI detectives gathered evidence against her was questionable.
The judges faulted DCI boss George Kinoti and his team for going against lawful procedures in collecting the evidence adding that due to the impropriety, the whole case against her had been contaminated.
The court, however, dismissed her plea to have the case dismissed based on the manner in which she was arrested.
The court also maintained that there was a legal and factual basis to the charges against the DCJ.
The DCJ was facing charges of abuse of office, forgery and failure to pay taxes to KRA for four of her properties acquired between 2014 and 2016.
DPP to challenge ruling lifting prosecution against DCJ Mwilu
The prosecution team led by Queen's Counsel Khawar Quereshi, declared taht they would be moving to court to challenge the High Court ruling.
The judges who acquitted DCJ Mwilu are Justices: William Musyoki, Mumbi Ngugi, Hellen Omondi, Francis Tuiyott and Chacha Mwita.
The Supreme Court deputy was defended by Senior Counsel James Orengo and lawyer Nelson Havi at the time.