Thomas Muller's first-half penalty and substitute Anatoliy Tymoshchuk's 79th-minute strike gave the Bavarians, who take on champions Borussia Dortmund on Saturday, their 12th win in 14 league matches to move on to 37 points with three games left this year.
The visitors never really hit top gear against battling Freiburg after coach Jupp Heynckes opted to rest Bastian Schweinsteiger ahead of Saturday's much-awaited showpiece match.
"Freiburg are a hard team to play against," Heynckes told reporters.
"But for long stretches we did it well, defensively we did not let anything through apart from the two chances they had."
Freiburg, who came into the match on the back of a four-game unbeaten run and had Fallou Diagne sent off in the 18th minute, dropped to tenth.
Gonzalo Castro scored twice as Bayer Leverkusen claimed their fifth win in six games with a 4-1 victory at Werder Bremen to move up to second place with 27 points.
Borussia Monchengladbach's Juan Arango scored a sensational goal in their 2-0 victory over VfL Wolfsburg, volleying in a 45-metre diagonal cross from the edge of the box. Gladbach move up to ninth on 20 points.
VfB Stuttgart are a point behind after edging past bottom-placed Augsburg 2-1 with Vedad Ibisevic heading in the winner in the 69th.
Toothless Hoffenheim slumped to a 4-2 defeat at Nuremberg, piling pressure on their coach Markus Babbel, whose team have won just one of their last nine games and are anchored in the relegation playoff spot.
Dortmund drew 1-1 with promoted Fortuna Dusseldorf on Tuesday to stay third on 26 with Schalke 04 in fourth place on 24 after slumping to a 3-1 away defeat against Hamburg SV.
GOMEZ START
With striker Mario Gomez making his first competitive start for Bayern since the Champions League final in May following ankle surgery in August, Bayern were instantly on the front foot.
The early atmosphere in all stadiums was muted with fans keeping quiet for the opening 12 minutes and 12 seconds in protest at new crowd security measures to be voted on on December 12.
The Bavarians were awarded a penalty for a handball in the 12th minute and Muller converted from the spot for his eighth goal of the season.
Freiburg were left with 10 men six minutes later after Diagne was sent off after receiving a straight red card for bringing down Xherdan Shaqiri.
Bayern controlled the game but needed a superb one-handed Manuel Neuer save to deny Max Kruse on the hour in a subdued second half.
With Bayern seemingly content to defend their slim lead, Ukrainian Tymoshchuk was given too much space to control a deep Philipp Lahm cross, round the keeper and tap in for his first goal of the season.
"It is extremely important to be top of the table in the winter," said Lahm, whose team has gone two seasons witho
