Portugal's Rui Costa (Lampre-Merida) finished third at the end of a hilly 256-km trek from Como to Bergamo.
After safely tackling the final climb up the Bergamo Alto, the 28-year-old Martin attacked with 450 metres remaining and caught his rivals off guard to snatch the win.
"I just love this race," Martin said. "It's one of my favourite races. It's just incredible to win it.
"I actually planned to attack on the last climb but I couldn't get through because there were too many people and the guys were going so hard anyway.
"I saw (Philippe) Gilbert and (Michael) Albasini – they are really fast - and Alejandro (Valverde) as well, so I needed to try something and the opportunity happened.
"Once I got the gap, it was so close to the line I just had to go as hard as I could and not crash on the last corner."
Dutchman Pieter Weening (Orica-GreenEdge) and Belgium's Ben Hermans (BMC) formed a two-man breakaway and built up a slender lead after navigating their way over the key climb of Berbenno.
But the duo were caught by the main peloton five km from the finish as they made their way up the final climb of the Bergamo Alto.
A host of riders, including BMC's Gilbert who was aiming for a third Lombardy win, launched attacks on the road into Bergamo but they were all powerless to resist Martin's late burst to the finish line.
By finishing second, Valverde displaces compatriot Alberto Contador (Tinkoff-Saxo) in the elite World Tour rankings ahead of the Tour of Beijing.The 34-year-old Valverde, who has 686 points, will take a 66-point advantage into the final race of the season which starts on Oct. 10.
(Reporting By Michael Hann; Editing by Rex Gowar)
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