Also freed by the anti-corruption court for lack of evidence were PSs Wilson Sitonik and David Onyonka.
Trial magistrate Lucy Nyambura declined to put the trio on their defence ruling that the prosecution failed to establish a case against them.
The magistrate held that there was no evidence that Magari did anything wrong in signing the contracts which were budgeted for.
She also found that Magari was not supposed to verify the said contracts before signing them as alleged by the prosecution.
Evidence tendered in court convinced the magistrate that Magari did not come into contact with the proposal of the disputed contracts.
“After analysing the evidence adduced this court is of the view that he did not do anything wrong in signing the contracts because he did so on the advice of former Finance Minster David Mwiraria,” she declared.
Sitonik and Onyonka, the magistrate observed, did not recommend the award of a passport issuing system contract to Anglo-Leasing Finance Limited.
There was also no evidence that Onyonka acted without regard to technical evaluation of the contracts by the user department in the Ministry of Home Affairs.
But former Home Affairs Permanent Secretary Sylvester Mwaliko had been put on his defence after the court ruled that he has a case to answer.
Mwaliko will now be put in the dock on March 15 to defend himself against allegations linking him to the scandal because the prosecution has made a case against him.
He was however acquitted over accusations that he gave false information to an official in the State Law Office seeking approval of the Anglo-leasing contracts.
The former senior civil servants had denied facilitating the award of a contract for installation of a new passport issuing system, valued at Sh7 billion.