Rahm shot 76 in the final round, but it was still enough for the two-time major champion to secure the season crown for the third successive year since joining LIV Golf.
"The last two weeks haven't been the best, have they," Rahm said. "I would say proud of earlier in the season.
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"To start off as well as I did with a few second places and not getting the win and then going to Hong Kong and getting it done when I needed to, having a lead and then basically losing it and birdieing four in a row in the last few holes was probably the most proud moment.
"It's been great. It's been a great year. Again, a little sour taste in my mouth because of how badly I played this week. But it's been something to be proud of.
"After last year and not getting the win, having possibly a question mark over the season-long race, to win twice and do it effectively and win it again definitely feels good."
Niemann, who won earlier this year in South Korea, went wire-to-wire at Trump International. He finished at 16-under 268.
Harold Varner III stayed with Niemann until the Chilean pulled away late with a birdie on the 13th and an eagle on the par-five 15th. Varner shot 70 to finish second.
"I feel like the more they push me, the better golfer I'm going to become from every experience that I have," Niemann said. "To be able to hit the shots that I did and make the putts that I did coming down the stretch, I put credit on myself."
Bryson DeChambeau shot 71 and tied for 38th, 23 shots off the lead. He cannot catch Rahm with one tournament remaining.
It capped a week in which LIV Golf CEO Scott O'Neil said it had signed a term sheet with a lead investor that will allow the league to move forward without Saudi Arabian funding. O'Neil did not identify the investor or the size of the investment.
