Try applying the brakes while sitting still. If the sound is still there then its the bushings/seals on the brake pedal.
Mine had this same low pitched squeak form the pedal. Every few months I crawl under the dash and apply some light oil to all of the pivot points and the grommets/boots on the brake pedal linkage.
If this is your issue go easy with the oil or spray lube as it can drip onto the pedals and cause your foot to slip off of the brake or accelerator while driving.