Slovenian rider Tadej Valjavec of the Lampre team came in second and Luxembourg's Frank Schleck of Team CSC finished third overall.
Italian Daniele Bennati of Lampre won Saturday's fifth and final stage, his third stage win having also taken the first and third.
'Sagan playing bumper cars' – How the big-name sprinters fared on Stage 2
Another Italian, sprint specialist Alessandro Petacchi, won the second stage, while Spaniard Alberto Contador won Friday's fourth stage, ahead of Valverde
'Almighty mess!' – Riders race to wrong line in awkward sprint
Giro d'Italia jersey rankings and standings