It was Johnson's 18th career PGA Tour victory and his second at the St. Jude Classic, which he also won in 2012.
Johnson finished with a flourish when his 171-yard second shot on the par-four 18th found the bottom of the cup, sending the crowd at the TPC Southwind in Memphis into a frenzy on a sweltering day.
"What a cool way to end the day to hole that shot on 18," Johnson said.
"I knew coming in this week that I was swinging really well and had a lot of confidence in my game. I played really well all week."
Johnson had led the rankings for 15 months before Thomas took over on May 13 and the win also moved him into second place in the PGA FedEx Cup standings.
Johnson started the day tied with Andrew Putnam but the 29-year-old American stumbled with a double bogey on the par-four first hole.
Although Putnam went bogey free for the final 13 holes, he was unable to match Johnson's brilliance and finished on 13 under par.
J.B. Holmes had five birdies and two bogeys for a final round 67 to end in third place. Stewart Cink and Richy Werenski tied for fourth at eight under par.
Johnson will be among the favourites to win the U.S. Open starting on Thursday at the Shinnecock Hills Golf Course in New York and he is confident of repeating his 2016 victory in the year's second major.
"I feel like my game is in good shape," he said.
"I'm driving it well, I'm really hitting my irons well, my wedges are really good, so I'm really looking forward to going into next week.
"I haven't seen the golf course yet but I'll get in 18 holes tomorrow and go from there."
(Reporting by Rory Carroll, editing by Ed Osmond)
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