The 21-year-old carded a one-under 69 to win his second major of 2015 by one shot on five under after Dustin Johnson three-putted the last from 12 feet.
South Africa's Louis Oosthuizen sank six birdies in his last seven holes in a 67 to tie with Johnson for second.
World number one Rory McIlroy (66) briefly threatened but ended level par.
Spieth, who remains on course to become the first player to win all four majors in a calendar year, is the youngest player to win the US Open since Bobby Jones in 1923.
He is the fourth-youngest player to win two majors and the sixth to win the Masters and US Open in the same year.
Butterfingers Spieth dropped the lid off the trophy shortly after being handed it
"I'm in shock but I feel for Dustin," said Spieth. "It's cool to be able to have two legs of the grand slam now, and to conquer golf's hardest test - the US Open is conquering the hardest layout in all of golf.
"I didn't have my best ball-striking at all and really grinded over those four or five-footers - that was the difference."
Johnson said: "I did everything I was supposed to do. I hit the ball really well. I just really struggled getting it in the hole. I didn't think I was hitting bad putts, they just weren't going in."
