The move was expected after Brees had a strong preseason and first-round draft pick Philip Rivers missed 29 practices and two exhibition games because of a holdout.
Rivers' holdout caused him to be named the third-string quarterback behind 41-year-old Doug Flutie.
Brees, the Chargers' opening day starter the past two years, completed 31- of-45 passes for 432 yards, three touchdowns and two interceptions in four preseason games. In 15 total series, he led the Chargers to five touchdowns and a field goal.
Last year, Brees was benched for five games and pulled from others. He ended the season 205-of-356 for 2,108 yards with 11 touchdown passes and 15 interceptions.