The 70-year-old has signed a one-year contract to replace Claudio Ranieri, who was sacked in November following an embarrassing defeat against the Faroe Islands.
Makarian – a former Peru and Paraguay coach – is charged with the task of turning Greece's fortunes around when their qualifying campaign recommences in March.
"The allocation of responsibility to be coach of the national team, for me is a great honour," said the Uruguayan.
"I want to thank the Federation, who chose me for this position.
"We have a difficult task ahead of us, but I believe in my work, as well as the Greek footballers."
Greece are bottom of Group F with just one point from four games and Ranieri paid the price when he was relieved of his duties after just four months in charge.
