Yildirim -- Fenerbahce chairman since 1998 and one of the most prominent and powerful figures in Turkish football -- had been charged with match-fixing and forming a criminal group to set the results of matches in the 2010/2011 season.
He had been sentenced to six years and three months in prison in 2012 over the scandal and served around a year of that sentence, before being freed pending appeal.
A retrial was then ordered in June 2014. Prosecutors requested earlier this week that all the suspects including Yildirim should be acquitted and their original convictions quashed.
"This process has been going on for four years and three months," Yildirim was quoted as saying in a brief statement to the court.
"It's about fighting for the honour of a group of people. I want me and all my friends to be acquitted."
Yildirim was acquitted of all charges, the state-run Anatolia news agency reported.
The Hurriyet daily said 13 other suspects were also acquitted in the hearing and a huge cheer erupted in the courthouse when Yildirim's acquittal was announced.
Hundreds of Fenerbahce fans, decked out in the famous canary-yellow colours of the club, demonstrated outside the Istanbul courthouse in support of Yildirm.
Dozens of Turkish football administrators and players have been arrested as part of the initial probe in 2011 into the 2010/2011 season that saw Fenerbahce win the title ahead of arch rivals Trabzonspor on goal difference.
His original conviction for match-fixing sent shockwaves through Turkish football and resulted in the club being banned for two seasons from European competition.
Undeterred by the legal problems, Yildirm has over the last months sought to spearhead a drive to turn the club into a major footballing power signing stars including Robin Van Persie and Nani from Manchester United.
His supporters ridiculed the original investigation against him, linking it to prosecutors who in 2013 brought sensational corruption allegations against the inner circle of President Recep Tayyip Erdogan.
Erdogan has angrily denied those claims, blaming the now dropped graft investigation on a "parallel state" led by his arch enemy, the US-based preacher Fethullah Gulen.