Kaepernick -- starting a second straight game in place of the concussed Alex Smith -- completed 16-of-25 passes for 231 yards with a TD pass and an interception, while also rushing for 27 yards with a score on six carries.
Frank Gore ran the ball 19 times for 83 yards as the 49ers (8-2-1) logged their second straight win.
The 49ers' Donte Whitner and Ahmad Brooks helped out on defense with interception returns for touchdowns.
The Saints (5-6), meanwhile, saw their three-game winning streak snapped despite three TDs and 267 passing yards from Drew Brees.
The New Orleans quarterback also surrendered the two interceptions, however, and was sacked five times.
Notable deaths of 2014 [PHOTOS]
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