Fans gathered outside the writer's home in the north Italian city applauded as Eco's coffin, laden with white roses, was carried to the imposing 15th century citadel and laid in state in a courtyard, under a presidential guard.
Musicians played Arcangelo Corelli's Baroque sonata "La Follia", a favourite which Eco used to play on the clarinet, before dignitaries including the cultural and education ministers paid homage to one of Italy's most loved sons.
"It was a piece that accompanied us always, my husband loved it very much," Eco's widow Renate Ramge said.
Eco, who had been suffering from cancer, passed away at home late on Friday at the age of 84.
The philosopher and semiotics lecturer who once famously described writing best-selling, heavyweight novels as "something I do at the weekends" lived within a maze of bookshelves, more vast library than house - and one he knew inside-out.
"You could see in his silences that he was consulting the unending library he carried within. Thank you Maestro for having spent your life looking out of the window for us," said Cultural Minister Dario Franceschini.
Friends remembered a gentle man who enjoyed whisky and wordplay in equal measure and had a nice line in self-deprecating humour, with one of his grandsons standing up to say how proud of his grandpa he was.
'Lost a master'
Some speakers choked back tears as they addressed the crowd in front of large heraldic flags sent by cities across Italy in a gesture of respect. Others told jokes they had shared with the intellectual.
"We have yet to fully understand his greatness. He was a friend and I thank him for having cared so much," said Elisabetta Sgarbi, head of the publishing house which will release Eco's last book on Friday.
La Nave di Teseo, which announced the release date on its Facebook page, is a new publishing house that emerged after notable writers, including Eco, moved to protect their independence and editorial diversity.
"Eco is the symbol of that innovative classicism which is so essential and which our country brings to the world. We have lost a master but we have not lost his teachings," Education Minister Stefania Gannini said.
Eco was revered around the world, largely thanks to "The Name of the Rose", the blockbuster novel that became a hit film starring Sean Connery in the role of a medieval monk with the detective brilliance of Sherlock Holmes.
"The Name of the Rose", which has been translated into 43 languages, has sold more than 10 million copies.
A Gothic murder mystery set in an Italian medieval monastery, it combines semiotics, biblical analysis, medieval studies and literary theory.
Eco leaves his wife, a German art teacher whom he married in 1962, and a son, a daughter and grandchildren.