The four-time African Footballer of the Year defeated rival Seidou Mbombo Njoya, the fourth vice-president at the Confederation of African Football.
Seven candidates should have contested the elections, but five of them pulled out on the morning of the elections.
Eto'o, 40, has promised a wide range of reforms to thrive the sport.
"We have to bring footballers to the centre of our policies," he said afterwards. "It is our role to ensure that those who play this discipline make a decent living out of it."
The former Barcelona, Inter Milan and Chelsea star has also promised to construct at least 10 stadiums during his mandate.
"I've spoken to the business community and we're certain we'll get the right investors who can accompany us in fulfilling our goals," Eto'o had said prior to the polls.
Eto'o's candidacy had triggered popular attention with the proceedings of the gathering broadcast live on national Cameroon television.
He will now be head of Cameroon's FA (Fecafoot) when the country hosts the Africa Cup of Nations in January and February.
Among those giving up their candidacy on Saturday morning were former Cameroon internationals Maboang Kesack and Jules Denis Onana.