Second baseman Cory Spangenberg, the Padres' No. 14 prospect, and another infielder, Tommy Medica, will also be on the team.
The Padres have four remaining spots on the roster -- all designated for pitchers -- that will be filled at a later date.
Hedges, who turned 21 on Aug. 18, has hit .157 in his first 16 games with Double-A San Antonio. He began the season with Single-A Lake Elsinore, where he hit .270 in 66 games.
"It's a chance to continue his development on both sides of the ball," said Randy Smith, the Padres' vice president of player development and international scouting. "Just as important as Austin facing better and more advanced pitching, he will be catching more advanced arms as well.
"[It's] a great opportunity for him to get another 75 at-bats and continue to soak in knowledge. We like the fact that he'll be catching our guys, and it will be easy for us to check his progress."
Hedges played in the Futures Game last month at Citi Field in New York and is considered one of the best catching prospects in professional baseball.
Spangenberg, the 10th overall pick in the 2011 Draft, began the season in Lake Elsinore, hitting .296 with a .364 on-base percentage. Spangenberg, 22, hit .276 in his first 69 games with San Antonio.
Medica, 25, is having a big season with San Antonio. He is hitting .282 with a .362 on-base percentage and has 15 home runs and 49 RBIs as a first baseman and designated hitter.
Opening Day for the Arizona Fall League is Oct. 8. The Javelinas will play their home games in Surprise as work continues on the Padres' and Mariners' new Spring Training facilities in Peoria.