The Dutchman, second in the first two stages, made his winning move in the closing 20 metres of the third stage into Messina, a city in the northeastern corner of Sicily.
Jan Svorada, of the Czech Republic, was second, followed by Italy's Massimo Strazzer, after the route of 176km from Catania.
Mario Cipollini, first to the line on Sunday and normally extremely competitive in sprint finishes, was content to arrive deep in the bunch, fell with about 50km when the leading riders tumbled, baulking the rest of the pack. He hurt his back in the spill, which involved about 20 cyclists, and lost precious time.
The defending champion Marco Pantani, who also won last year's Tour de France, and plenty of other favourites for final victory in the 22-stage race finished in the main group behind the sprinters and were credited with the same time as the winner.
Today's fourth stage is the first on Italy's mainland. The relatively flat route takes the riders 186km north from Vibo Valentia, near the toe of the boot, to Terme Luigiane.Reuse content