Sanchez attacked with team-mate Bauke Mollema, Richie Porte of Sky and Joaquim Rodriguez of Katusha with 7km to go from a group of about 20 riders - but Sanchez was the only one who stayed clear then he time-trialled his way to the line.
He had enough time to zip up his jersey and savour the victory as he finished six seconds ahead of the chasing group.
Gianni Meersman (Lotto-Belisol) won the sprint finish for second ahead of Simon Gerrans (Orica-GreenEDGE).
Sanchez, who also won this event back in 2010, has now won seven races this season with stage victories in both the Tour de France and Paris-Nice among his achievements.
Sanchez will not line up for Rabobank for the Vuelta a Espana that begins on Saturday. Robert Gesink will be their big hope in the final Grand Tour of the season.