An own-goal by Vasilis Lampropoulos condemned Greece to its third loss in six Nations League games, with Estonia winning 1-0 at the Olympic Stadium in Athens on Sunday.
The Greeks struggled to create chances against some staunch defending by the Estonians, whose physical approach made life difficult for the hosts.
Greece finished the group with nine points in six games, finishing third place behind Finland and Hungary, while Estonia was relegated to Division D.
The Greeks will now have to wait for the draw for the Euro 2020 qualifiers, which kick off in March 2019.
After Sunday’s result, Greece will be placed in the lowly Pot 4 in the December 2nd draw for the EURO qualifiers.