Businessman Ali Koc was elected new Fenerbahce chairman in a landslide ballot win among members, winning 16,092 of their votes compared to just 4,644 for Yildirim.
The change at the top marks a turning point for the Istanbul club, which has been dominated by Yildirim since he became chairman in 1998.
In a tense congress, held in a special stand erected on the pitch of Fenerbahce’s stadium, both men accused the other of lying and promised to pump investment into the club if elected.
Under Yildirim’s leadership, Fenerbahce have won the Turkish football league six times and have on occasion been fearsome opponents in Europe.
Yet recent years have brought thinner pickings, with the side’s last Super Lig championship win in 2014 and this season finishing runners-up to arch rivals Galatasaray.
The men’s and women’s basketball sides have however been all-conquering, with the men crowned Euroleague champions in 2017.
Yildirim was in 2012 sentenced to six years and three months in prison on charges of match-fixing in a scandal that rocked Turkish football.
But he and his supporters blamed the investigation on supporters of the US-based preacher Fethullah Gulen who Turkey accuses of staging the 2016 failed coup, charges Gulen denies.
He served one year of his sentence and in October 2015 was acquitted by an Istanbul court. The ruling still requires approval by Turkey’s supreme court and in this event Fenerbahce are expected to seek massive compensation for the losses caused.
Koc’s candidacy represented a rare intervention in Turkish public life by his family, one of the country’s richest but most low-key industrial dynasties.
The third son of former Koc Group chairman Rahmi Koc, Ali Koc, has promised to use his business contacts to reinvigorate the club.
His eldest brother Mustafa, the former Koc Group chairman, died in 2016. His other brother Omer currently leads the group.
Some commentators have compared the Fenerbahce election to Turkey’s presidential polls on June 24, where President Recep Tayyip Erdogan is seeking a new term after 15 years in power in the face of a strong challenge from secular opposition candidate Muharrem Ince.