A source told SI.com Wednesday night that the decision to start Kaepernick wasn't based on health. His first career start came in Monday's 32-7 rout of the Chicago Bears.
Kaepernick started in place of Smith, who is suffering from a concussion he sustained in a Nov. 11 tie against the Rams.
"To me, it's the opposite of a controversy," 49ers coach Jim Harbaugh said.
Kaepernick went 16-for-23 for 243 yards and led the 49ers (7-2-1) to scores on their first four possessions Monday night.
After the game, members of the media asked Harbaugh who would start at New Orleans. He responded, "I usually tend to go with the guy that has the hot hand and we have two quarterbacks that have a hot hand."