At the Indianapolis event, Rahm shot a career-best 11-under 60 to take the clubhouse lead, only to lose in a playoff to Sebastian Munoz.
But the Spaniard still narrowly beat Joaquin Niemann, who tied for fourth in Indianapolis, to claim the season-long title for the second year running. Niemann won five events on the Saudi-backed tour in 2025, but Rahm's consistency prevailed.
After his 60 gave him the clubhouse lead at 22-under in Indianapolis, Munoz, who carded a historic 59 with a double bogey on Friday, birdied the final two holes for a 65 to force a playoff. Munoz clinched the event with a six-foot birdie putt on the first extra hole, the par-four 18th.
"It's a great moment, but it just doesn't feel great to finish the year losing two playoffs," Rahm said.
"I'm sure over time I'll get over that, and I'll really appreciate what I've done this year. To be able to win the season without actually winning a tournament, I know I'll be proud of that."
Niemann admitted it was tough to miss out on the overall title by such a narrow margin, as Rahm's consistent top-10 finishes across 12 of 13 events, including a crucial 60 in Indianapolis, edged him out by just 2.5 points in the season-long standings.
"It's kind of hard to swallow," he said.
"But at the end of the day, I think it is what it is. I feel like it's going to put something inside me to kind of work harder and try to be in this situation again next year and make it different."
Munoz and Niemann led Torque GC to the team championship, setting a record 64-under total. The LIV Golf season wraps up with the Team Championship in Michigan starting Friday.
Meanwhile, former Open champion Henrik Stenson was relegated after finishing tied 22nd and falling into the drop zone of LIV Golf standings. Stenson, who gave up the Ryder Cup captaincy in 2023 after joining the breakaway tour, will now need to go through qualifying to secure his place next season.
A late birdie surge by Ian Poulter ensured the Englishman survived at Stenson's expense, highlighting the fine margins in LIV Golf's standings and shaping the Team Europe lineup for the 2025 Ryder Cup.