BBC Sport, Lome
Gnassingbe finished third in the election on Tuesday
Rock Gnassingbe, son of the late leader of Togo, Eyadema, has been voted out of office as the president of the Togo Football Federation (FTF).
FTF delegates at Tuesday's extraordinary congress decided by 24 votes to 8 to replace Gnassingbe with Avlessi Adaglo Tata.
Former Prime Minister Messan Agbeyome Kodjo finished second after polling 14 votes amidst tight security.
In his election manifesto, Tata promised a development programme dedicated to youth football.
His financing of a US$6million stadium for his club Union Sportive Masseda seemed to have convinced voters of his commitment to develop the game in the West African country.
The elections were ordered by Fifa two months ago following a crisis in the federation.
The Gnassingbe-led FTF has been in turmoil since four executives members resigned following their disastrous outing at the World Cup in Germany in June.
Togo's maiden World Cup campaign, which ended in the first round, was marred by a dispute between the FTF and its player over bonuses and allowances.
This compelled Fifa to intervene and promise to pay the allowances out of Togo's $5.6 million World Cup appearance fee.