Now, a Church-appointed commission is picking up the charred pieces of the fiery friar. Savonarola's writings have been combed line by line and declared heresy-free; last week, his sermons were read out in Florence's Duomo for the first time since his death.
The commission is also extracting the truth about the man himself from a perplexing mixture of poison-pen histories and hagiography. "People who arouse such strong emotions are either loved or hated. Over the ages he has generated some very dodgy history on both sides," said Don Gianfranco Rolfi, the historian priest who heads the commission. "But the time is right for a reassessment of this complex monk."
The commission's report will be ready by autumn. If, as appears likely, it is favourable, the preacher who persuaded artists such as Botticelli and Fra Bartolommeo to heap their more sensual works on "the bonfire of the vanities", along with other Florentine frippery, will be well on his way to sainthood.
At the time of his execution, the Dominican ascetic had been banned from the pulpit, had been ridiculed in his own church by high-spirited local lads, and had seen the city's administration - a council installed according to his own proto-democratic vision - turn its back on him to toady to the hated Pope in Rome.
Eight years before, in his heyday, this gloomy, unprepossessing monk from Ferrara had convinced Florentines of their city's destiny as the New Jerusalem. Unappealing as it may seem today, his creed of strict abstinence, clean living and a return to the simplicity of the early Church was welcomed by citizens weary of the intrigues and profligacy of their Medici rulers.
Paintings that made the Virgin Mary "look like a harlot" should be thrown out of churches, he thundered from the pulpit of the church of San Marco. Ostentatious clothes should be banned, prostitutes - "pieces of meat with eyes" - should be punished, and sodomites should burn at the stake.
Such highly coloured accounts, says Don Rolfi, have painted Savonarola as a medieval throwback and the scourge of the Renaissance, and have masked his more serious theological and social achievements. It is this side of the friar, not the firebrand of popular mythology, that was celebrated in the streets of Florence last week with marches, debates and flowers cast symbolically into the Arno from the Ponte Vecchio.
The chief organiser of these festivities, Don Enzo Mazzi, has every reason for harbouring a sneaking sympathy for Savonarola: he angered the Vatican when he sided with rioting students in Florence in 1968, setting up an alternative community that survives to this day. Savonarola's "far-sighted modernity" prompted him to take up the monk's cause.
"What Savonarola preached was not religious fundamentalism, it was the idea of a community founded on the common good," said the priest. "For him, government needed the participation of the people to make it legitimate. This was a far cry from what we would consider democracy, but in an age when despotism was the norm, it was a big step in that direction."
Why has it taken five centuries for Savonarola's merits to be recognised? "We have records of saints venerating Savonarola as a saintly man long ago, but at a popular level, the monk inspired too much passion to permit calm discussion until now," said Don Rolfi.
If, in the past, that passion was overwhelmingly hostile, today the tide of public opinion in Florence has turned. Egged on by the civil society to which Savonarola attributed such importance, the same church that 500 years ago brought about his destruction may make this intense visionary monk the saint for the next millennium.