Ryan racked up 275 yards with one interception, hitting Tony Gonzalez nine times for 91 yards and a score.
Michael Turner picked up 80 yards and scored a touchdown on 14 carries for the Falcons, who logged a 3-0 start to the season for the first time since 2004.
Thomas DeCoud led Atlanta's defense with a fumble recovery and two interceptions.
The Chargers (2-1) were led by Philip Rivers, who managed 173 yards with two interceptions while going 21-of-38.
Jackie Battle led San Diego's running backs with 55 yards on just three carries.