Itemere and the twelve were let off the hook following an application by the Office of the Director of Public Prosecutions (ODPP) Igonga to have them released.
While granting the application Onyina argued that the prosecution bears the burden of proving the case beyond reasonable doubt.
"Since there is no objection from the defence over the same, the court being an impartial arbiter cannot refuse to grant the prayers as the bearer of the mandate to prosecute has been satisfied with the evidence presented to withdraw the charges," said the chief magistrate.
He ordered that the 13 individuals be discherged from the counts they were facing and securities deposited by them released.
In his application seeking withdrawal, the ODPP said there was no sufficient evidence to sustain the charges. However, the state said it will present additional charges against Savula and his wives Melody Gatwiri and Hellen Jepkorir. The three are out on Sh2 million, and Sh 1 million bond and Sh500,000 cash bail respectively.
Savula and his wives were listed in the case as directors of Sunday Publishers Limited, Melsav Company Limited, Johnnewton Communications, Express Media Group, No Burns Protection Agencies Limited, Cross Continents Ventures Limited, and Shiledlock Limited, entities which are said to have irregularly received the Sh122.3 million.
Also charged was Dennis Chebitwey who at the time was heading the Government Advertising Agency (GAA).
The arrest and presentation in court of Savula and his co-accused followed a probe ordered by then DPP Noordin Haji over an editorial published by one of the dailies in which the paper demanded for action against GAA for failing to pay Sh2.5 billion owed to various media houses.
Two other accused persons - Tabitha Nyamboke and Henry Mungasia have since died in a case that saw arraignment of 30 individuals who faces charges ranging from abuse of office, theft, conspiracy to steal and conspiracy to commit a felony.
Savula was further charged with making a false document with an intention to irregularly acquire the sum from the State Department for Broadcasting and Telecommunications.
Already 13 prosecution witnesses have given their evidence with only nine remaining . Hearing of the case resumes on April 22.
The prosecution side yesterday applied to have the charge sheet amended to exclude the 13 who have been acquitted and also give a chance to the defense counsels to prepare for their defense on the remaining 9 prosecution witnesses.
The request was allowed by the court.
"We are making an application to amend the charges before the hearing dates, change the numbering of accused persons and add additional charges to some of the accused persons," said the prosecution.
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The defense counsel asked to be given the amended charge sheet at least three days before the resumption of the case so as to prepare for their defense on the remaining 9 prosecution witnesses.
The request was allowed by the court.
During the hearing last year a former GAA director Ngare Gituku told magistrate Onyina that he was not aware of conspiracy by Savula and 29 others to defraud the government of the said Sh122.3 million.
"There was immense pressure from advertisers and an audit was conducted to verify the genuine pending bills owed to various media houses. If any payment was made it was because there were approvals and paper trails supporting payments," said Gituku.
The former GAA boss who was being cross-examined by the defence counsel, said there was evidence to support payments made to Savula and his companies and that the advertisements deserved to be compensated for.