The award, announced Thursday and voted on by the Baseball Writers' Association of America, went to Giants catcher Buster Posey.
Headley's fifth-place finish was the highest by a Padres player since Adrian Gonzalez finished fourth in 2010.
The lone San Diego player to win the award was Ken Caminiti in 1996. Since then, only Gonzalez in 2010 and Greg Vaughn (fourth) in 1998 have finished in the top five of the voting.
Headley led the NL with 115 RBIs to go with his 31 home runs and .286 batting average. He finished the season on a roll, capturing the NL's Player of the Month award in August and September.
With those torrid months of August and September, Headley became the first player in franchise history to knock in 30 or more runs in a month twice.
"There have been so many more opportunities," Headley said in October of getting chances to hit with runners on base. "The second half has been incredibly enjoyable, especially being around these guys."
While his offensive numbers are impressive in themselves, the fact that he compiled them while playing half his games in pitcher-friendly Petco Park makes them even more amazing.
"To have that [production] in San Diego, that's pretty amazing," Brewers manager Ron Roenicke said in October. "He needs to be talked about a lot more than he has been. To have that kind of year in that place? Phenomenal."
During the offseason, Headley worked on getting more loft on the ball and flew to Tennessee to work with new Padres hitting coach Phil Plantier.
"It's fun to watch a guy figure it all out and see him piece it together," Plantier said. "I don't see any reason why this isn't going to be normal production for him for the rest of his career. This is not a fluke. This is very real."
|Buster Posey, Giants||27||4||1||422|
|Ryan Braun, Brewers||3||15||10||4||285|
|Andrew McCutchen, Pirates||6||13||11||1||1||245|
|Yadier Molina, Cardinals||2||6||8||13||1||1||241|
|Chase Headley, Padres||1||9||7||5||5||1||127|
|David Wright, Mets||7||4||1||3||4||3||86|
|Adam LaRoche, Nationals||6||5||2||5||1||86|
|Craig Kimbrel, Braves||1||3||5||2||2||3||1||73|
|Aramis Ramirez, Brewers||1||1||4||6||1||47|
|Jay Bruce, Reds||2||1||3||2||1||46|
|Matt Holliday, Cardinals||1||1||2||2||3||2||34|
|Aroldis Chapman, Reds||1||1||1||3||2||20|
|Brandon Phillips, Reds||2||1||1||1||18|
|Joey Votto, Reds||1||1||1||5||16|
|R.A. Dickey, Mets||1||2||2||1||16|
|Clayton Kershaw, Dodgers||3||1||1||15|
|Ian Desmond, Nationals||1||2||2||1||15|
|Michael Bourn, Braves||1||2||12|
|Allen Craig, Cardinals||2||2||10|
|Gio Gonzalez, Nationals||1||1||8|
|Alfonso Soriano, Cubs||1||1||1||8|
|Kris Medlen, Braves||2||8|
|Martin Prado, Braves||2||1||8|
|Ryan Zimmerman, Nationals||1||1||7|
|Giancarlo Stanton, Marlins||1||1||7|
|Carlos Beltran, Cardinals||1||6|
|Aaron Hill, Diamondbacks||1||2||6|
|Carlos Ruiz, Phillies||1||1||4|
|Jason Heyward, Braves||1||2||4|
|Johnny Cueto, Reds||1||2|
|Bryce Harper, Nationals||1||2|
|Chipper Jones, Braves||1||1|
|Miguel Montero, D-backs||1||1|
|Angel Pagan, Giants||1||1|
|Hunter Pence, Giants||1||1|
Steve Gilbert is a reporter for MLB.com. Follow him on Twitter @SteveGilbertMLB. MLB.com reporter Corey Brock contributed to this report. This story was not subject to the approval of Major League Baseball or its clubs.