Ryan Blaum and Andrew Putnam each shot 64 and were tied for second, and C.T. Pan (65) and Wesley Bryan (66) followed at 8 under.
"I have high expectations going into every week", Johnson said when asked about the U.S. Open.
"I mean winning this week, I think is bigger confidence booster than being number one in the world", Johnson added.
It was Johnson's 18th career PGA Tour victory and his second at the St. Jude Classic, which he also won in 2012.
Brooks Koepka, a week before defending his U.S. Open title, carded 69 to slip five strokes behind, while Phil Mickelson (70) fell six adrift.
While numerous game's elite are having this week off to prepare for the U.S. Open, Johnson chose to play his way into the second major championship of the year at Shinnecock Hills.
Holding a four-stroke lead over second-place finisher Adam Putnam, all Johnson had to do on the 18th hole was avoid catastrophe on a historical level. Teeing off in the afternoon when the wind was stronger, Nordqvist closed her bogey-free round with a birdie on the par-5 ninth. "I've earned my way here and I feel like it's going to be a fun day".More news: Justify's value skyrockets to $60M with Triple Crown win
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"Statistically, you feel like you should have made holes in one all the time out here as much as you play but they don't come around very often", the 2009 British Open champion said.
Johnson had already shown off his ludicrous velocity earlier in the day by hitting a 307-yard drive with an iron on the hard par-4 10th hole.
"I knew I was swinging well", Johnson said after his round. "I played really well all week".
Yokomine, the victor of 23 events on the Japan LPGA Tour, flirted with a 59 but parred the par-5 18th for a 61 to tie the course record.
He's now won nine PGA Tour events since June 2016. John Daly withdrew before the second round.
In a final walkthrough before heading off to Shinnecock Hills and the Open, Dustin Johnson sauntered to a six-stroke victory in the FedEx St. Jude Classic on Sunday to reclaim from Justin Thomas No. 1 in the World Golf Ranking.