Johnson finished with a 30-under par total of 254 at TPC Boston, with Harris English a distant second on 265 after a closing 69.
Johnson’s 22-under third-round total had given him the largest 54-hole lead on tour this season — five strokes — and he was quick to build on it on Sunday.
He set the tone with an eight-foot eagle putt at the second, tapped in for birdie at the fourth and rolled in a four-foot birdie at the fifth.
Birdie putts of 10 and 13 feet at the seventh and eighth saw him make the turn five-under for the day, and he rolled in another four-foot birdie at the 12th.
The only thing that slowed him was a weather delay of an hour and 15 minutes, the horn sounding just after he teed off on 17.
He returned and birdied the par-five 18th in fading light and steady rain.
Former US Open champion Johnson toppled Spain’s Jon Rahm from the top of the rankings, and will also lead the US tour’s FedEx Cup standings going into the second playoff event, the BMW Championship.
South Africa’s Louis Oosthuizen grabbed the final spot in the 70-man BMW field with a birdie at the final hole on Sunday, capping a two-over 73 that put him in a tie for 13th and knocked Doc Redman out of the top 70 in the playoff standings.