DeGrom received 26 of 30 first-place votes. Cincinnati Reds center fielder Billy Hamilton and St. Louis Cardinals second baseman Kolten Wong finished second and third, respectively, in the voting conducted by the Baseball Writers' Association of America.
DeGrom, 26, went 9-6 with a 2.69 ERA and 144 strikeouts in 140 1/3 innings pitched over 22 starts.
DeGrom initially was called up to the majors to work out of the bullpen. Instead, he excelled in starts as a side-muscle injury kept Dillon Gee on the disabled list. As a result, deGrom pitched the remainder of the season as a starter.
"I was just thankful to be in the big leagues this year," deGrom said. "Receiving this award was a great honor."
Pitching coach Dan Warthen praised deGrom's poise on the mound as a rookie.
"You know the antiperspirant commercial? You never see him sweat," Warthen said.
"When you put Jacob in there with Wheeler and Harvey, they should all be synonymous," Warthen said.
DeGrom was twice named NL Rookie of the Month, and he also tied a MLB record by striking out the first eight batters he faced against the Miami Marlins on Sept. 15.
The Mets drafted deGrom in the ninth round of the 2010 draft. He became the fifth Rookie of the Year in franchise history, joining Tom Seaver (1967), Jon Matlack (1972), Darryl Strawberry (1983) and Dwight Gooden (1984).
Hamilton, 24, hit .250 with six home runs, 48 RBIs and a team rookie-record 56 stolen bases.
Hamilton stole a combined 155 bases in 2012 while still in the minors. That set a new Minor League Baseball single-season record for steals.
ESPNNewYork.com's Adam Rubin contributed to this report.