Middlebrooks, obtained by general manager A.J. Preller last winter, was optioned on July 21 to Triple-A El Paso, where he hit .255. Middlebrooks wasn't added to the roster in September, which may have signaled the end of his time with the organization.
The Padres also non-tendered catcher Rocky Gale and left-handed reliever Frank Garces.
The Padres also avoided arbitration with infielder Brett Wallace, signing him to a one-year deal for $1 million.
Wallace, who signed with the Padres last winter as a Minor League free agent, hit .302 in 64 games after being recalled from El Paso on June 19.