Kraft was the underdog against the No. 1 world ranked amateur Cantlay in Sunday's 36-hole final.
Cantlay has engineered a superb run on the PGA Tour by recording four top 25 finishes and shooting a second round 60 at the Travelers Championship.
Both American finalists are awarded a spot in the 2012 US Open and are traditionally also invited to The Masters. Kraft will also get a spot in the British Open.
Kraft, who just finished his senior season in US college golf, took the lead when Cantlay bogeyed the 16th hole.
On the par-five 18th hole, both players drove it into the bunker.
Kraft and Cantlay chipped out safely, but Cantlay had the longer approach shot and left it a little short of the green. Kraft found another bunker with his approach.
Cantlay then left his chip shot well short of the hole, and Kraft blasted his sand shot close to the pin.
Cantlay missed his par putt and conceded the hole -- and the match -- to Kraft.
