The news means Washington is no longer affiliated with Class A Vermont.
"We are delighted to add Auburn to the Nationals' family," team president Stan Kasten said in a statement. "This agreement again narrows the footprint of our Minor League system, and starting next summer, Auburn and the Doubledays' fan base will get their first glimpse at the rewards reaped from both our scouting and player-development systems."
By partnering with Auburn, the Nationals' Class A affiliate is now closer to Washington, and just 35 miles west of Syracuse, the Nationals' Triple-A affiliate.
The Doubledays play in 2,706-seat Falcon Park, which opened 1995 and includes arguably the best home clubhouse in the New York-Penn League. The team is named after Abner Doubleday, the Civil War general and Auburn, N.Y., native who has often been credited with inventing the game of baseball.
The Doubledays -- whose run of six consecutive Pinckney Division titles (2002-07) was capped by a league championship in 2007 -- recently ended a working relationship with the Blue Jays.
Johan Santana, Roy Oswalt, Luis Gonzalez, Aaron Hill, Kenny Lofton and Rick Dempsey are among those who played stints for Auburn during their Minor League careers.