Scheffler is the first back-to-back winner of the prestigious Jack Nicklaus Award since Tiger Woods in 2006-07.
The world No.1 had the best statistical season since Woods by leading the tour in all the important categories from tee to green, along with scoring.
What he lacked, compared to Rahm, was tournament wins.
Scheffler won The Players Championship and the Phoenix Open. So remarkable was his consistency that Scheffler did not finish worse than 12th until July.
But Rahm won four times, including his second major when he captured the Masters.
The PGA Tour said voting took place from December 1 through December 15. Rahm, who for 18 months had been an ardent supporter of the tour, announced he was joining the Saudi-funded rival league on December 7.
The tour said Scheffler received 38 per cent of the vote in what was believed to be a tight race.
It did not disclose the voting percentage received by Rahm, FedEx Cup champion Viktor Hovland, US Open champion Wyndham Clark or Rory McIlroy.
The tour previously did not release any vote totals for the award. Now it withholds what percentage of players voted.
In another close race, Eric Cole won the Arnold Palmer Award as rookie of the year over Ludvig Aberg, of Sweden.
Cole was the only player to reach the second round of the FedEx Cup playoffs, a longtime player in golf's minor leagues who made $US5 million ($A7.4 million) in his first year on tour.
Aberg didn't turn pro until June. He won the season-ending RSM Classic by tying the PGA Tour scoring record for 72 holes at 253.
He previously won on the European tour and went from leaving Texas Tech in June to playing in the Ryder Cup for the victorious Europe team in September.
