Chiriboga, 70, who ran the soccer federation for 18 years but has been under house arrest since late 2015, was convicted of money-laundering along with two others at the organization.
He is one of about 40 soccer bosses, mainly Latin Americans, implicated in U.S.-led investigations that have rocked FIFA.
Judge Miriam Escobar said about $6.1 million had passed illegally through Ecuador's soccer federation.
Her court in the capital Quito ordered the three soccer officials to pay back double that and to give up properties.
Lawyers for the men said they would appeal.
Chiriboga, who has denied the charges, would be likely to serve his sentence at home given his advanced age.
(Reporting by Jose Llangari and Alexandra Valencia; Writing by Andrew Cawthorne; Editing by Sandra Maler)
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