Lawyers for Bukola Saraki argued prosecutors had failed to establish a case alleging that he made a false declaration of his assets before and after his tenure as governor of Kwara state.
He was also accused of collecting double salaries during his time as governor of the western state from 2003 to 2011 and as a senator after he stepped down.
The case had been heard at the Code of Conduct Tribunal, which tries cases of alleged abuse in public office.
Judge Danladi Umar said in his ruling that the prosecution "failed to link the defendant with the commission of the offences as charged".
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"All the responses of the prosecution witnesses and evidence in this trial have been discredited as a result of cross-examination and have become unreliable," he added.
In the light of the foregoing, the tribunal has nothing to do other than to discharge and acquit the defendant."
Under Nigerian law, senior politicians including state governors are required to declare their assets when they enter office.
He was not the preferred candidate for Buhari's ruling All Progressives Congress (APC), which led to claims the charges against him were politically motivated.
Saraki, who is Nigeria's third-most powerful politician behind Buhari and Vice-President Yemi Osinbajo, was last year acquitted in a separate case of conspiracy and forgery.
It was alleged the 54-year-old former banker and his deputy falsified parliamentary rules to get elected.