Molinari joined Charles 'Chick' Evans (1916), Bobby Jones (1924, '30), Gary Cowan (1966) and Chris Patton (1989) as amateur champions at Merion, which hosted its 17th U.S. Golf Association championship.
The finalists earned an invitation next year to the Masters and the U.S. Open, and, as the winner, Molinari gets a return trip to the British Open, where he finished 60th this year at St. Andrews.
Molinari, a 24-year-old engineering student, faced a three-hole deficit after 18 holes, but struck quickly in the final round. He birdied three of the first five holes to even the match and took his first lead on the 25th hole, the 345-yard seventh, with a 3-foot birdie putt.
He curled in a 35-foot birdie putt at the ninth to move to 2-up and extended his lead to 3-up at No. 11 with about a 40-footer.
After halving three straight holes, Molinari closed out the match on the 15th with a long birdie putt. He took a step toward the hole and, as the ball disappeared into the cup, unleashed a sweeping uppercut in celebration.
Dougherty, a senior from Northwestern who was cheered by his purple-clad teammates and coach, had a chance to extend the match, but missed a 20-foot birdie try on almost the same line as Molinari.
Molinari shook Dougherty's hand, and then turned and embraced his father, who had flown from Italy to follow his son in the final rounds.Edoardo Molinari of Italy defeated American Dillon Dougherty, 4 and 3, on Sunday to capture the U.S. Amateur Championship at Merion.
'It means a lot to me. I think I still have to realize it completely,' said Molinari, who became the first European to win the Amateur since Harold Hilton of England took the title in 1911. 'I'm really, really happy to have this win and to have won it here, especially.'
Dougherty held a 3-up lead after the morning 18, but Molinari won the first two holes of the afternoon with birdies. He squared the match with a par at the fifth, then took the lead with a 9-foot birdie putt at No. 7.
Molinari won the ninth and 11th to move 3-up. That was all he needed as the duo halved the next four holes to give Molinari the most prestigious amateur title.
'I think a very big turning point was seven, eight and nine because after the seventh, I finally was 1-up in the match and I had been trailing all match long,' said Molinari. 'I just tried to stay as calm as possible all week long.'
Molinari now gets an invitation to the Masters, U.S. Open and British Open as long as he stays an amateur. Molinari indicated that he will accept those offers rather than turn pro and try his hand at European Tour qualifying school.
'I think I will have a lot of fun next year playing all of these very good tournaments and then I'll probably turn pro after the British Open next year,' said Molinari.
Dougherty also gets an invite to Augusta and the U.S. Open and was philosophical following the loss.
'I knew after 18, Edoardo had been playing well all week, and I knew he was going to play much better than he played in the morning, or at least I planned on it,' said Dougherty. 'I played pretty solid and he just played unbelievably.'