Accent Jobs-Wanty rider Napolitano took advantage of a crash inside the final five kilometres of the 175.4km stage from Brugge to Harelbeke to claim victory in a bunch sprint.
Tom Van Asbroeck (Topsport Vlaanderen-Baloise) was second and Barry Markus (Vacansoleil-DCM) third.
Omega Pharma-Quick-Step's Mark Cavendish was denied a seventh win of 2013 as he finished 23rd.
OPQS worked to bring an early escape group back into the peloton's midst to enable Vandewalle to preserve his lead.
That group consisted of Jelle Wallays (Topsport Vlaanderen-Baloise), Jean-Pierre Drucker (Accent Jobs-Wanty), Niels Wytinck (An Post-Chainreaction) and Christoph Pfingsten (Rijke-Shanks).
After 56km they had a lead of 3:56 which was then steadily eroded. It was down to under two minutes with 40km remaining then 44s with 21km to race.
"They (my riders) were organised for the sprint, but there was a crash inside the final 5km and it involved Gert Steegmans," OPQS sport director Tom Steels said.
"So our leadout was a little bit compromised. It was also really dangerous as there was a lot of tailwind, making it a hectic and high speed sprint.
"Cavendish tried, but not 100 percent as it was a bit too risky. But, okay, Kristof maintained his jersey as OPQS controlled the race today. We will see tomorrow for the last stage."
Eight Radioshack-Leopard Trek riders were forced to ride on spare bikes after an overnight theft.
1 Danilo Napolitano (Ita) Accent.Jobs - Wanty
2 Tom Van Asbroeck (Bel) Topsport Vlaanderen - Baloise
3 Barry Markus (Ned) Vacansoleil-DCM
4 Kenny van Hummel (Ned) Vacansoleil-DCM
5 Jarl Salomein Bel) Topsport Vlaanderen - Baloise
6 Gediminas Bagdonas (Ltu) AG2R-La Mondiale
7 Adrien Petit (Fra) Cofidis
8 Kenny De Haes (Bel) Lotto Belisol
9 Dylan Groenewegen (Ned) Cyclingteam De Rijke - Shanks
10 Yves Lampaert (Bel) Topsport Vlaanderen - Baloise