The defending champion, Pavel Tonkov, retained the overall lead, preserving his one-second lead over his fellow Russian, Evgeni Berzin.
Cipollini dominated a crowded sprint following a 156-kilometre (96.7- mile) ride from San Marino to Arezzo displaying the impressive power and speed which has earned him the nickname of "Super Mario."
The 30-year-old edged out another Italian, Endrio Leoni, and Angel Edo Alsina, of Spain.
Cipollini, who won the two first stages of the Giro at the weekend, lost the leader's pink jersey to Tonkov on Monday, following an uphill individual time trial won by the Russian.
The stage, through a hilly course crossing from the Marche to the Tuscan region, saw several spills in the final kilometres. The casualties included Colombia's Celio Rocancio, Italy's Gabriele Colombo and the Russian Vladislav Bobrik, who suffered bruises but completed the stage.