The emerging Cannondale rider took the seventh edition of the race, finishing six seconds ahead of team-mate Peter Sagan with Rinaldo Nocentini (Ag2r-La Mondiale) third.
After departing the village of Gaiole in Chianti, deep in Tuscany’s wine-producing area, Giairo Ermeti (Androni), Aleksejs Saramotins (IAM), Maxim Belkov (Katusha) and Michael Schar (BMC) attacked.
Going under the Flamme Rouge, the latter trio were still in the lead but they had been joined by Moser and the 22-year-old had the power in the extremely demanding final kilometre, with gradients reaching 16%, to take the victory on the famous Campo.
Prolific Slovak Sagan, who won the GP Citta di Camaiore on Thursday, escaped out of the chase group to follow his team-mate - who won five races in his debut professional season last year - over the line.
Ermeti, Saramotins, Belkov and Schar built up a two minute lead as they crossed the first of the eight sections of unpaved roads that characterise the 190km race.
They extended that advantage to 10:20 but after the sixth unpaved section, that lead had been whittled down to little more than two minutes with Juan Antonio Flecha having escaped from the chase group behind.
But the Spaniard was caught by Moser on the penultimate white-road section where the riders went sharply up the Colle Pinzuto.
Moser left Flecha on a steep ramp on the final upaved section and went in pursuit of Schar and Belkov, who had left their fellow long-time escapees, on the 12km run-in to the finish.
With 6km remaining Moser had dragged Saramotins up to Schar and Belkov and they had a small advantage on an elite chase group ahead of the race-deciding final climb.
Moser soon made his move inside the city walls of the UNESCO World Heritage town to take a famous victory with Radioshack Leopard’s Fabian Cancellara back in fourth.
The Swiss star was trying to obtain an historic third victory in the Strade Bianche to add to his previous victories in 2008 and 2012.
Moser said: “My attack was instinctive. In races like this, isn’t time or space for too many tactics. I saw the pace relent for a moment and attacked. Sagan was the rider everyone had to watch, and I exploited that.” “In the final kilometres I had to risk losing. None of the riders ahead of me would give me any help. They were probably right. When I saw the group arrive from behind, I was afraid, but I didn’t panic. I should also say that I kept cool because I knew that Peter [Sagan], of those behind me, would certainly have won the race. So it was about the team today. "I’ve always thought this race suited me. Even in the youth categories, I saw that, when the racing became individual, I was always competitive. In this sense I can say I resemble my uncle Francesco [Moser, the 1977 World Champion and Classics great].”