Johnson, who had a three-shot overnight lead, fired a five-under 68 for a 16-under 203 total on another blustery day at the Kapalua Resort to finish four shots clear of defending champion Steve Stricker (69).
"Obviously it gives me a lot of confidence going into this year," Johnson, the first player since Tiger Woods to win at least one tournament in six consecutive years straight out of college, said. "I'm very pleased to come out and get a win this week, I played very good golf the last two days.
"It's tough when you have a three-shot lead to stay aggressive. I just hit a couple of bad drives that cost me a few shots but other than that I played really good golf today."
The weather-hit event was trimmed to three rounds and forced to a rare Tuesday finish because of relentless howling winds.
The elite field of champions from last year's US PGA Tour completed 36 holes on Monday after play had been abandoned the previous three days because of strong winds.
Stricker, who carded an error-free round, got to within a shot of his US Ryder Cup team-mate with five holes to play but could not keep up the rally as Johnson went on to collect his seventh career win.
American Brandt Snedeker, last season's FedExCup champion, had a solid start to his 2013 campaign, also closing with a 69, to finish alone in third, six shots back of Johnson.
Masters champion Bubba Watson (71) was a further shot back in a tie for fourth with fellow American Keegan Bradley (70).
Holding a four-shot lead through eight holes, Johnson saw his lead chopped to two when he bogeyed the ninth and Stricker birdie the same hole.
Johnson's roller coaster back nine ride continued with a birdie at the 12th before taking another nosedive with a double-bogey at 13 to leave the steady Stricker just one off the pace.
But Johnson immediately hit back in spectacular fashion, chipping in for an eagle two at the par-four 14th followed by birdies at 15 and 18 to close out a final round that was nearly as wild as the Hawaiian weather.
"I had some opportunities if I could have made some putts early in the round and a couple on the backside as well but all-in-all it was a pretty good round," said Stricker, who battled a shooting pain down his left side all tournament and will take time off to have it treated.
"He (Johnson) played well when he had to. ... I knew it was going to be tough today but I gave him a bit of a run for a little while."