The 31-year-old was discovered hours before his team were scheduled to play Udinese in a Serie A match. He is believed to have died from a cardiac arrest
As soon as the coffin was brought back out, the people in the square again raised their scarves, sang the Fiorentina anthem and chanted Astori's name as well as 'c'e solo un capitano' (there's only one captain).
Astori's mother blew a kiss to the crowd, while the people of Florence were also thanked by his brother Marco in his eulogy.
Earlier, fans gathered by Fiorentina's Artemio Franchi stadium and applauded loudly as Astori's coffin was driven past. There were shouts of his name and 'grande capitano' (great captain), while a banner held up read: 'Per sempre nostro capitano (forever our captain)'.
Astori, who played for Italy 14 times, leaves behind his long-term partner, Francesca Fioretti, and their two-year-old daughter. A tearful Fioretti was seen making her way into the church on Thursday morning with Astori's family, including their daughter, Vittoria.
The Fiorentina players were met by applause when they arrived on foot, led by midfielder Milan Badelj.