The Lampre man came out on top by a bike's length after the 163km stage which began and finished in Alzira.
An escape group, featuring Thomas Voeckler (Bouygues Telecom), Adrian Palomares (Fuerteventura) and Emanuele Sella (Panaria), went off before the only climb of the day - the Alto de Barceheta after 20km.
But they were reeled in over the second half of the race setting up the inevitable bunch finish which concluded with a second win this season for the 26-year-old following his success in the second stage of the Mediterranean Tour
Dombrowski sent to hospital for suspected concussion, Giro participation in doubt
Panaria sprinter Paride Grillo was prevented from starting after producing a high level of hematocrit.
'Sagan playing bumper cars' – How the big-name sprinters fared on Stage 2
'Almighty mess!' – Riders race to wrong line in awkward sprint