The 49ers moved within reach of a playoff spot, which they will clinch if New Orleans loses to St. Louis Monday night.
It was the second shutout in three weeks for the 49ers (10-3), who blanked Buffalo, 35-0 on Dec. 2 but suffered a 27-14 loss to the St. Louis Rams last week.
"I love the way our defense is playing," 49ers coach Steve Mariucci said. "They are playing smart and aggressive."
San Francisco last had two shutouts in a season in 1974. It also marked the first time Miami has been blanked twice in a season since 1970. The Dolphins suffered a 24-0 loss to the New York Jets on Nov. 18.
The Dolphins (9-4) remained in first place in the AFC East, but had their lead cut to a half game over New England (9-5). Miami plays at New England next Saturday.
"When you are playing another team that has nine wins, you've got to come out and be on top of your game and we were not," Dolphins coach Dave Wannstedt said. "There are no excuses for not playing better today. We've got to get ready for next week. We'll probably be playing for the division."
When the Dolphins last visited here in 1992, the 49ers rolled to a 27-3 win and Jerry Rice set the NFL record for career touchdown receptions.
This time, the 49ers dominated again, relentlessly hounding Fiedler, who was intercepted three times, sacked five times and fumbled once.
"They gave us a couple of line stunts that got us, they gave us a couple of blitzes that we weren't able to figure out or pick up," said Fiedler, who completed 16 of 28 passes for 149 yards.
San Francisco controlled the ball for more than 39 minutes and held the Dolphins to just 12 first downs and 174 total yards.
Third-year defensive end Chike Okeafor, who had four career sacks, led the pass rush with 2 1/2 sacks and safety Zack Bronson had two interceptions.
"The defense did a tremendous job and we got another shutout," Bronson said. "We came in here and showed everyone that we can play with anybody."
While Barlow reached the end zone twice, Garrison Hearst rushed for 103 yards on 26 carries to surpass 1,000 yards in a season for the fourth time in his career. It appeared Hearst's career was over following five operations for a broken ankle which caused him to miss the previous two seasons.
"Can you imagine what Garrison has achieved?" Mariucci said. "For us to think that he was going to be this dominating and this on top of his game after all he's been through with five surgeries is quite a story. He's so productive, and he's such a leader and such fun to be around."
Miami managed just four first downs and 54 total yards in the first half. Fiedler threw for a mere 25 yards while Garcia completed 12 of 17 for 83 yards.
"The defense if doing great, period," Garcia said. "It's great to have the defense playing the way they are. It gives us great opportunities to win games."
The 49ers effectively ended the game with a 17-play, 98-yard drive which consumed more than 11 minutes in the third quarter. Garcia hit Terrell Owens with a 28-yard pass and Garrison Hearst rushed seven times for 39 yards before Barlow scored his second touchdown of the game.
"They beat us in all phases of the game today -- offense, defense, special teams," Dolphins safety Brock Marion said. "They're a very good team. You've got to give them credit."
"I will take nothing from their performance, they played very well," Smith said. "We couldn't establish a ground game, but the loss was a team loss. No one facet lost it for us exclusively. This loss was a team effort. We're a better team than this but we have to prove it."
Miami cornerbacks Sam Madison and Patrick Surtain were able to contain Owens, who had four catches for 43 yards. Owens has 82 receptions for 1,139 yards.