Tour de France champion Bradley Wiggins dropped out of contention, finishing more than 3 1/2 minutes behind the main pack as he struggled with a cold.
Cavendish clocked just over 3 hours along the 83-mile route from Longarone to Treviso, which started with a few hills and ended with a long, flat finish around a circuit.
It was Cavendish's third win in this year's race. The British rider with the Omega Pharma-Quick Step team also won the first and sixth legs.
Nacer Bouhanni of France and Luke Mezgec of Slovenia crossed second and third, respectively, with the same time.
In the overall standings, Nibali, an Italian with Astana, remained 41 seconds ahead of 2011 Tour winner Cadel Evans of Australia. Wiggins' Sky teammate Rigoberto Uran of Colombia is third overall, 2:04 behind.
It was the 13th Giro stage win of Cavendish's career and his 39th in cycling's three Grand Tours - the Giro, Tour and Spanish Vuelta.
Stage 13 Friday is the race's longest, a mostly flat 158-mile leg from Busseto to Cherasco, with a few hills shortly before the finish.
The race hits the mountains again over the weekend, with Saturday's stage climbing Sestriere and Bardonecchia and Sunday taking riders into France and up the Col du Galibier, which is often included in the Tour de France.
The race ends May 26 in Brescia.
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