Knost, who played at Southern Methodist, is only the second golfer to win both the Amateur and the U.S. Public Links titles in the same year. Ryan Moore did it in 2004.
After a tumultuous 36-hole final match in which both players held a late lead, Knost put a tricky 45-foot chip within 3 feet on The Olympic Club's 17th hole. Thompson conceded a short par putt moments later, and Knost thrust both arms in the air before hugging Thompson, who might be his teammate next month on the American entry in the Walker Cup.
Knost, who won the Publinx championship in June, took the lead for good with a 15-foot birdie putt on the 13th. He then holed a tough chip shot on the 14th, pumping his fist as it rattled home from the back of the fringe to put him 2 up on the historic course on the rolling hills south of San Francisco.
Knost and Thompson both earned spots in the 2008 fields at the Masters and the U.S. Open with their semifinal victories. Knost still hasn't decided whether he'll wait to use those amateur berths instead of turning pro, which he originally planned to do after the Walker Cup in Northern Ireland.
Thompson pulled closer with a birdie on the 16th, but put his 17th approach shot well down the hill past one of the Olympic's tough raised greens.
Knost was only 1 up after an unremarkable first 18 holes, and the stocky 22-year-old seemed frustrated with himself, muttering and stalking around the course.
Thompson evened the match when he bounced a circus shot off the lip of a bunker to within 3 feet to save par on the third hole of the second 18. Thompson went ahead on the fifth, holing a hard-breaking 45-foot birdie putt.
But Knost cleared his head in time to go back ahead on the eighth with an easy birdie -- his first birdie of the day that wasn't conceded.
Thompson, a Tucson, Ariz., native who plays at the University of Alabama, still hasn't been chosen for one of the two remaining spots on the Walker Cup team with Knost, who earned his spot with his Publinx title.
Thompson planned to fly out of San Francisco for Tuscaloosa on Sunday night, with an accounting class waiting for him on Monday morning.