Revered across Greece's political spectrum, Glezos was most famous for scaling the steep walls of the Acropolis with a friend in 1941 to take down the swastika and replace it with the Greek flag.
It was the first visible act of resistance against the Nazis, who occupied Greece between 1941 and 1944. He was sentenced to death in absentia.
Glezos died of heart failure at a central Athens hospital, where he was admitted on March 18.
Greek Prime Minister Kyriakos Mitsotakis led tributes to Glezos, calling him a "lionheart" and "the sweetest man."
"The death of Manolis Glezos leaves Greeks poorer, but the legacy of his life leaves Greece richer," he said in a statement.
"His example, that of a true patriot and fighter, is a guiding light for us all. And it gives us the strength to unite to overcome difficulties, like those we are experiencing today," Mitsotakis said, referring to the coronavirus crisis.
Former left-wing Prime Minister Alexis Tsipras said: "He will live on through eternity as the symbol of a fighter who knew how to sacrifice himself for his fellow man."
With his white mane of hair and thick moustache, Glezos was a recognizable fixture in leftist politics.
In his late eighties, he braved police teargas at protest rallies against tough cuts imposed in exchange for international bailouts that kept the Greek economy afloat between 2010 and 2015.
A member of the Socialist PASOK Party which he represented in the European Parliament, Glezos gradually migrated further to the political left.
At the age of 91, in 2014, he became a member of the European Parliament representing Syriza, the left-wing party which came to power in 2015. He resigned a year later.
Asked what had kept him at the forefront of politics for so long, Glezos told Reuters in 2012 that it was the memories of dead comrades.
"Before every battle, every protest, we told each other: 'If you live, don't forget me'. I am paying a debt to those I lost during those difficult years. My only regret is that I haven’t done more."