Soto, the steady catcher who helped the Cubs win the NL Central title, got 31 of 32 first-place votes. The other went to Cincinnati's Joey Votto.
Called up from the minors in April, Longoria batted .272 with 27 homers and 85 RBIs despite missing five weeks after breaking his right wrist Aug. 7. Confident at the plate and splendid on defense, he was a big reason for the Rays' stunning surge to the World Series after 10 straight losing seasons.
Chicago White Sox second baseman Alexei Ramirez was the runner-up after receiving 18 second-place votes. Boston outfielder Jacoby Ellsbury finished third.
Soto hit .285 with 23 homers, 35 doubles and 86 RBIs. He became the first catcher to win Rookie of the Year in either league since Mike Piazza of the Los Angeles Dodgers in 1993.
The previous winner from the Cubs was pitcher Kerry Wood 10 years ago.
The Rays were so sure Longoria would become a big star that they gave him a $17.5 million, six-year contract after only six major league games. The deal could be worth up to $44.5 million over nine seasons.
So far, Longoria has delivered.
Tampa Bay started play in 1998 and had never won more than 70 games until Longoria helped lead the Rays to 97 wins this year and the AL East title. He also hit a tying double with two outs in the eighth inning during the July All-Star game at Yankee Stadium.
After his injury, Longoria, who turned 23 last month, returned to the lineup in time for Tampa Bay's playoff run. He homered in his first two postseason at-bats against the Chicago White Sox, then connected four times against Boston in the AL championship series to set a rookie record with six homers in one postseason.
But his offensive tear ended in the World Series, when Longoria went 1-for-20 with nine strikeouts and two RBIs as the Philadelphia Phillies beat Tampa Bay in five games.
The 25-year-old Soto had a disappointing October after his team compiled the best regular-season record in the National League. He went 2-for-11 (.182) without an RBI as Chicago was swept in the first round by the Dodgers, leaving the Cubs still searching for their first pennant since 1945 and first World Series championship since 1908.
Voting for BBWAA awards is conducted without regard to postseason performance. Votto came in second with 21 second-place votes and 76 points to Soto's 158.
In July, Soto became the first National League catcher to start an All-Star game.
The NL Cy Young Award will be announced Tuesday.