Braun, Milwaukee's slugging third baseman, edged Colorado shortstop Troy Tulowitzki by two points in balloting by the Baseball Writers' Association of America.
Pedroia, the little Boston second baseman with the big swing, easily topped Tampa Bay outfielder Delmon Young. Voting was done before Pedroia helped lead the Red Sox to the World Series title.
Called up from Triple-A in late May, Braun hit .324 with 34 home runs and 97 RBIs. The Brewers led the majors in homers this season and stayed in contention for the NL Central championship until the final week.
Braun got 17 of the 32 first-place votes and finished with 128 points. Tulowitzki received 15 first-place votes and had 126 points.
Braun's .634 slugging percentage led NL players and was the highest by a rookie in major league history. He did not have enough plate appearances, however, to qualify for the title.
His big offensive numbers were enough to overcome 26 errors, tied for most in the majors with Minnesota shortstop Jason Bartlett.
Tulowitzki led big league shortstops in fielding percentage, got to many more balls than anyone at his position and turned an unassisted triple play.
Tulowitzki also set an NL rookie record for home runs by a shortstop (24), and batted .291 with 99 RBIs as the Rockies surged to the NL pennant.
There was a tie for the NL award in 1976 between San Diego's Butch Metzger and Cincinnati's Pat Zachry -- though the voting format was different then. Last year, Florida shortstop Hanley Ramirez beat out Washington third baseman Ryan Zimmerman by four points.
"Ryan Braun came to the major leagues and had as much offensive impact as I have seen in my 12 years as a general manager," Milwaukee's Doug Melvin said. "To show you how good Ryan was, in any other year Troy Tulowitzki would have won hands down."
Braun, who turns 24 this Saturday, became the second Brewers player to win Rookie of the Year. Pat Listach won in 1992 when Milwaukee was in the American League.
Pedroia got 24 of the 28 first-place votes and finished with 132 points. Young was next with three first-place votes and 56 points and Kansas City pitcher Brian Bannister received the other first-place vote.
Pedroia hit .317 with eight home runs and 50 RBIs. Generously listed at 5-foot-9, he led off the World Series opener with a home run -- voting was completed at the end of the regular season.
A month into the season, Pedroia was hitting just .172 with no home runs and only two RBIs. His slump was so severe that some Red Sox fans were calling for Alex Cora to take over the starting spot.
The 24-year-old Pedroia perked up in May and his all-out style made him a fan favorite at Fenway Park. His diving stop on a grounder by Miguel Tejada helped preserve Clay Buchholz's no-hitter in September.
Pedroia became the sixth Red Sox player to win the AL award and first since Nomar Garciaparra in 1997.
The AL Cy Young Award will be announced Tuesday. Boston's Josh Beckett and Cleveland's C.C. Sabathia are co-favorites.