The former Italian champion, riding for Astana, edged Jelle Vanendert (Lotto-Belisol) and Peter Sagan (Liquigas-Cannondale) to the line at the end of the undulating 256.5km route in the Limburg region.
Thirty one climbs peppered the route which criss-crossed the hills to the east of Maastricht in the latest UCI WorldTour one-day race but the action boiled down to the last of those, the Cauberg.
Philippe Gilbert, who was aiming to become just the second cyclist in the 47-year history of the race to win the event three times, led a group of around 35 riders up the 1200m climb - with a painful maximum gradient of 13% - in pursuit of Oscar Freire.
The treble world champion attacked with 6km remaining after day-long escapee Romain Bardet (AG2R) had finally been caught.
Gilbert, who also won Fleche Wallonne and Liege–Bastogne–Liege in 2011 to claim all three Ardennes Classics, faded in the closing stages and it looked like the highly fancied Sagan was going to take a maiden Classics victory as Spaniard Freire was caught in the final 100m.
But Gasparotto, who was third in this race in 2010, came around the other side to win ahead of Belgian Vanendert.
"Two years ago I was third here and I've learned from my mistakes that day," Gasparotto said.
"Back then I tried too hard, too soon on the Cauberg, this time I waited right until the last minute.
"It's my most important win since I took the Italian National Championships back in 2005.
"(Double winner) Philippe Gilbert started his sprint very early because he wanted to close the gap on Oscar Freire.
"Sagan was strong, but he faded in the last few metres."
Frenchman Bardet along with Pello Bilbao (Euskaltel), Michel Kreder (Garmin), Alex Howes (Garmin), Steven Caethoven (Accent Jobs), Cedric Pineau (FDJ), Simone Stortoni (Lampre), Sébastien Delfosse (Landbouwkrediet) and Eliot Lietar (Topsport Vlaanderen) escaped early and opened up a maximum lead of 13 minutes.
That advantage was down to 4:40 by the time they commenced their second ascent of the Cauberg with 75km remaining and they splintered on the final loop.
Howes was finally dropped by Bardet on the penultimate climb, the Keutenberg, 12km from the finish whilst behind the peloton had been whittled down to an elite group although it was missing Tour de France champion Cadel Evans, who abandoned the race, and Olympic champion Samuel Sanchez who was dropped on the 27th climb, the Kruisberg.
Bardet's brave solo bid to win the 47th edition of the race came to an end with 8km remaining and then Freire launched a counter-attack but the real fireworks were yet to come with the Katusha rider having to settle for fourth, followed by Thomas Voeckler (Europcar) and BMC's Gilbert.