Some riders heard the news before they began the stage but many others, including eventual winners Team Sky, only found out after they had celebrated victory on the podium.
Everyone was shocked and race organizers have announced that a minute's silence in memory of Ballerini will be held before stage two on Monday morning.
Many riders expressed their condolences via Twitter.
"I think that everyone who has the luck to know Franco Ballerini feels like a piece of his heart has died today! An hug to his family!" Liquigas rider Manuel Quinziato wrote from Qatar.
Robert Hunter: "I just been shocked by the news of Franco Ballerini's passing! He taught me so much about being a pro, a person I'll never forget!!!"
Lance Armstrong: "So sad to hear of passing of Franco Ballerini. Raced many years w/ him. Cool guy and great champ. Leaves behind a wife and 2 kids. RIP, FB."
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Charly Wegelius: "Today is a sad day. My heart is with the children and wife of Franco Ballerini. He was a gentleman and a true champion."
Italians remember Ballerini
In Italy, the news of Ballerini's sudden death shocked the cycling family. Ballerini was loved by everyone for his understanding character and genuine affection.
Paolo Bettini rushed to the hospital in Pistoia after he heard the news. He and Ballerini had competed in several rally events together, as pilot and navigator. They were very close after winning two world titles and a gold medal at the 2004 Olympic in Athens.
"I've lost a great friend, a brother," Bettini told Italian media after comforting Ballerini's wife Sabrina.
"Ballerini had risked his life a thousands times in races. He rode Paris-Roubaix without a helmet (when they were not obligatory) and dived down descents in the Dolomites, but he never had any problems."
"Destiny took him now while he was enjoying himself because he really enjoyed car racing. He was the one who got me into rally racing. Yet he was always careful after safety. He never took any risk." Cipollini struggles to take in the news
Ballerini had only been national coach for a few months when Mario Cipollini won the world title in Zolder in 2002.
"I just can't get used to the idea that Franco is dead. I just keep thinking that something will bring him back to life," Cipollini told La Gazzetta dello Sport.
"I keep thinking of all the moments of joy we shared together and especially in Zolder in 2002 when he created the perfect tactic and created the perfect team to give me the world title."
"Every high-level athlete like Franco always seeks out thrills, even after they've retired because it helps them feel competitive, that's how Franco explained his passion for rally racing. He still felt the adrenaline flow and as well as using it as national coach, he also let it out in car races."
Ballerini was very close to former Italian national coach Alfredo Martini. The veteran coach took his fellow Tuscan under his wing and taught him all he knew about uniting the Italian riders together into a strong team for the world championships. The two would often travel to races together and consult on team selection before the world championships.
"Franco was like a son to me. He came to my house two or three times per week for a coffee, to say hello or a chat. He was one of the family. I'll always remember that when the Italian Cycling Federation President asked me for a list of possible candidates. I told him, 'I'll give you just one name: Ballerini.'"
