Kaepernick carried the ball seven times for 54 yards and went 10-of-16 through the air for 164 yards as the 49ers (6-2) scored 30 or more points for the fifth straight game -- all of them wins.
Frank Gore also scored twice on the ground, carrying the ball 19 times for 71 yards as San Francisco romped in the second of two scheduled NFL games in London this season.
Minnesota defeated Pittsburgh at Wembley Stadium Sept. 29.
The Jaguars (0-8), meanwhile, continued the worst start in team history as Chad Henne was limited to 228 yards on 29-of-45 efficiency.
2014: NFL Cheerleaders [PHOTOS]
Michael Sam cut from the Dallas Cowboys