The pile-up ruled sprint rival Andre Greipel out of contention, as Cavendish's Omega Pharma-Quick Step team dictated the latter stages and propelled their man to the win.
Alessandro Petacchi was a distant second with Peter Sagan finishing third as the race journeyed from Bucchianico to Porto Sant'Elpidio.
"It would have been nice to sprint against Kittel [who had already been dropped] and Greipel", said Cavendish afterwards.
Alberto Contador retained his overall lead of two minutes and eight seconds over Nairo Quintana.
Cavendish, Sagan and Greipel are expected to compete for victory in Sunday's Milan-San Remo after the gruelling Pompeiana climb was removed following adverse weather - a route change which will benefit the sprinters.
Stage six results
1. Mark Cavendish (Britain / Omega Pharma - Quick-Step) 4:16:15"
2. Alessandro Petacchi (Italy / Omega Pharma - Quick-Step) ST
3. Peter Sagan (Slovakia / Cannondale)
4. Arnaud Demare (France / FDJ.fr)
5. Tony Hurel (France / Europcar)
6. Robert Wagner (Germany / Belkin)
7. Kristian Sbaragli (Italy / Team MTN)
8. Bartosz Huzarski (Poland / NetApp)
9. Mark Renshaw (Australia / Omega Pharma - Quick-Step)
10. Davide Appollonio (Italy / AG2R)
1. Alberto Contador (Spain / Tinkoff - Saxo) 25:17:51"
2. Nairo Quintana (Colombia / Movistar) +2:08"
3. Roman Kreuziger (Czech Republic / Tinkoff - Saxo) +2:15"
4. Julian Arredondo (Colombia / Trek) +2:39"
5. Jean-Christophe Peraud (France / AG2R) +2:40"
6. Mikel Nieve (Spain / Team Sky) +2:50"
7. Daniel Moreno (Spain / Katusha) +2:51"
8. Domenico Pozzovivo (Italy / AG2R) +2:56"
9. Giampaolo Caruso (Italy / Katusha) +2:58"
10. Robert Kiserlovski (Croatia / Trek) +3:06"
- Sports & Recreation
- Peter Sagan
- Mark Cavendish
- Andre Greipel
- Omega Pharma
- Alessandro Petacchi
- Alberto Contador
- Nairo Quintana