The 24-year-old American also joined Jack Nicklaus, Tiger Woods and Spieth as the only players since 1960 to earn five wins, including a major, in a season before the age of 25.
World number one Johnson, who won the award last year, had four wins in the 20 events he entered, including triumphs at the lucrative World Golf Championships-Mexico Championship and World Golf Championships-Dell Technologies Match Play events.
Johnson, whose red-hot run of three consecutive wins was interrupted after being sidelined by a back injury suffered on the eve of the U.S. Masters in April, enjoyed eight top-10 finishes in the season and was fourth in the FedExCup playoffs.
Spieth, who was named the PGA Tour's Player of the Year in 2015, had victories at the British Open, where he earned his third career major title, AT&T Pebble Beach Pro-Am and Travelers Championship.
The 24-year-old Texan also recorded 12 top-10 finishes, which tied Thomas for most this season. He also had top-10 finishes in all four FedExCup playoff events in 2017.
Japan's Matsuyama had earned victories at the World Golf Championships-HSBC Champions, Waste Management Phoenix Open and World Golf Championships-Bridgestone Invitational and finished eighth in the FedExCup.
Voting for the honour, known as the Jack Nicklaus Award, will close on Oct. 2, with the winners to be announced that week.
Wesley Bryan, Patrick Cantlay, Mackenzie Hughes, Grayson Murray and Tour Championship winner Xander Schauffele were the five nominees for the PGA Tour's Rookie of the Year award.
Both awards are determined by a member vote, with PGA Tour members who played in at least 15 official money events during the 2016-17 season eligible to participate.
(Reporting by Frank Pingue in Toronto; Editing by Christian Radnedge)
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