The US Open champion took the lead in the second round and never relinquished it, ending the weekend 17 under par and winning by five shots at Riviera Country Club.
Johnson needed to win and hope Jason Day finished lower than a three-way tie for third to top the rankings - and the outgoing number one could only manage a tie for 64th after finishing two over par.
The leaders had to complete two rounds on Sunday, following storms on Friday.
Johnson took to the course on day four with a one-shot lead but was six strokes clear after the third round.
The 32-year-old started with a birdie on the first and picked up further shots on the fifth, eighth and 12th before birdieing the last three holes for a seven-under 64.
The 17-year-old Thomas, ranked 94th in the World Amateur Golf Ranking, topped the standing released yesterday, with Australia’s Fred Lee second and South African Garrick Higgo in third place.
The Junior Presidents Cup is a new initiative by the PGA Tour on the lines of the popular Junior Ryder Cup, which is played the week before the biennial tournament between Europe and USA, and features the top junior players from the two teams.
When informed about his standing in the list by Sport360, Thomas was surprised. “I knew I’d be in the list, but I thought I would be around the fifth or sixth place. To be on top of the standings is a huge surprise.
“I am so looking forward to the tournament. I am hoping to play some of the big American amateur events this year, but the Junior Presidents Cup is going to be massive.
“I love the team competitions like the Ryder Cup and Presidents Cup. Hopefully, one day I will get to represent the International Team in the real Presidents Cup. But until that happens, to make it to the Junior Presidents Cup is a big objective for me.”
The Junior Presidents Cup will be played among the top-12 junior American players against the top-12 non-European juniors on September 25-26, at Plainfield Country Club in Edison, New Jersey. The American team will be captained by the 18-time major champion Jack Nicklaus and the International boys will be led by South African legend Gary Player.
The boys will then be invited to witness the Presidents Cup between Fred Couples-led Team USA and the Nick Price-led Internationals.
The International Team will be made up of the leading 11 qualified players based on the World Amateur Golf Ranking (WAGR) as of August 3, 2017. The 12th and final spot will be awarded to the leading player on the WAGR list as of September 6, 2017, who is not otherwise qualified. The players must not have reached their 19th birthday or not graduated from high school as of January 1.
Tiger Woods has admitted the combined toll of multiple operations on his battered body means he doesn't think he "will ever feel great" again.
But the former world number one said he hoped to be able to compete for titles and majors in the future.
"I feel good, but not great," said Woods, 41. "Granted, I don't think I'll ever feel great because it's three back surgeries, four knee operations."
The 14-time major-winner returned from a 16-month injury lay-off in December and has slumped to 674 in the world rankings.
"I am always going to be a little bit sore, it's just the way it is. But as long as I can function and function at a good enough level then I'm fine with that," he said.