Pelucchi pipped France's Arnaud Demare in a bunch sprint to claim the second stage spoils, with Omega Pharma - Quick-Step's Cavendish finishing safely in the lead group to add to his team time trial win on Wednesday.
At one point Cavendish had looked out of contention after being held up by a crash involving Marcel Kittel - but he managed to rejoin the main group, although was unable to contest the finish.
Cavendish thanked his fellow riders for allowing him to retain his overall lead.
"I was behind Kittel when he crashed at a narrow little roundabout," he said afterwards.
"The peloton split because of it. Some gentlemen in the peloton gave me a hand to move up, but I got to the front with 500m to go, before the sprint even started, and I was already on the limit."
Pelucchi's win is IAM Cycling's first World Tour stage victory.
Stage two was 166 km ride between San Vincenzo and Cascina.
Stage 2 result
1. Matteo Pelucchi (Italy / IAM Cycling) 3:56:12"
2. Arnaud Demare (France / FDJ.fr) ST
3. Andre Greipel (Germany / Lotto)
4. Sam Bennett (Ireland / NetApp)
5. Peter Sagan (Slovakia / Cannondale)
6. Davide Appollonio (Italy / AG2R)
7. Filippo Fortin (Italy / Bardiani Valvole)
8. Sacha Modolo (Italy / Lampre)
9. Tony Hurel (France / Europcar)
10. Kristian Sbaragli (Italy / Team MTN)
11. Robert Wagner (Germany / Belkin)
12. Danilo Wyss (Switzerland / BMC Racing)
13. Andriy Grivko (Ukraine / Astana)
14. Nicola Ruffoni (Italy / Bardiani Valvole)
15. Roger Kluge (Germany / IAM Cycling)
16. Johan Vansummeren (Belgium / Garmin)
17. Mark Cavendish (Britain / Omega Pharma - Quick-Step)
18. Jack Bauer (New Zealand / Garmin)
19. Tom Veelers (Netherlands / Giant)
20. Juergen Roelandts (Belgium / Lotto)
21. Maciej Bodnar (Poland / Cannondale)
22. Tanel Kangert (Estonia / Astana)
23. Michal Kwiatkowski (Poland / Omega Pharma - Quick-Step)
24. Simon Clarke (Australia / Orica)
25. Richie Porte (Australia / Team Sky)
26. Rigoberto Uran (Colombia / Omega Pharma - Quick-Step)
27. Patrick Gretsch (Germany / AG2R)
28. Andrew Talansky (U.S. / Garmin)
29. Nairo Quintana (Colombia / Movistar)
30. Alberto Contador (Spain / Tinkoff - Saxo)
1. Mark Cavendish (Britain / Omega Pharma - Quick-Step) 4:16:25"
2. Michal Kwiatkowski (Poland / Omega Pharma - Quick-Step) ST
3. Rigoberto Uran (Colombia / Omega Pharma - Quick-Step)
4. Mark Renshaw (Australia / Omega Pharma - Quick-Step)
5. Alessandro Petacchi (Italy / Omega Pharma - Quick-Step) +2"
6. Tony Martin (Germany / Omega Pharma - Quick-Step) +3"
7. Simon Clarke (Australia / Orica) +11"
8. Daryl Impey (South Africa / Orica)
9. Svein Tuft (Canada / Orica)
10. Ivan Santaromita (Italy / Orica)
11. Michael Hepburn (Australia / Orica)
12. Luke Durbridge (Australia / Orica)
13. Cameron Meyer (Australia / Orica)
- Sports & Recreation
- Omega Pharma
- Mark Cavendish