The 33-year-old Guevara was one of the most popular players on Toronto, playing 46 games in two-plus seasons for TFC.
His nine goals are tied for third with Chad Barrett all-time on TFC, behind only Danny Dichio (14 goals) Dwayne De Rosario (11). His 10 assists are tied for first with Marvell Wynne.
Guevara has returned to Honduras, where he signed with Motagua.
TFC also declined options on Argentine forward Pablo Vitti and Haitian defender Lesly Fellinga.