The visitors went in front in the 42nd minute as Thomas Müller slammed home a rebound from inside the area after Luca Toni had a shot stopped by Simon Pouplin.
The lead increased to 2-0 in the 68th minute when Du-Ri Cha fired past his own goalkeeper on an attempted backpass after Müller's cross from the right.
Stefan Reisinger pulled a goal back in the 90th minute for Freiburg, but they could get no closer, leaving Bayern to claim three points.
BERLIN (AFP) - Bundesliga leaders Bayer Leverkusen were held 0-0 at second-placed Hamburg while Bayern Munich moved up to fifth as hot-shot midfielder Thomas Mueller helped seal a 2-1 win at Freiburg.
The stalemate at Hamburg's HSH Nordbank Arena left the top two locked on 21 points with Bayer top by virtue of goal difference.
"We came here to get points and we could have won it at the end," said Leverkusen's ex-Liverpool defender Sami Hyypia.
"Maybe we could have done more with the ball, Hamburg had their chances, but from our point of view, we defended well.
"We knew Hamburg would push us hard, so we are happy to take a point from here.
"Hamburg are strong and we knew we had to stay tight at the back, we played very well in defence, but we could have done better in attack."
Hamburg coach Bruno Labbadia admitted his side suffered from their horrendous injury list. Related article: Injuries cripple Hamburg
Hamburg have laboured under a growing injury list with defenders Alex Silva, Collin Benjamin and Miroslav Stepanek plus striker Paolo Guerrero all suffering torn cruciate knee ligaments.
Defender Bastian Reinhardt (foot) and forward Mladen Petric (ankle) are also ruled out for the rest of the first half of the current campaign.
"We had to set the tone of the match, Leverkusen sat back and waited for us to make the first mistake," said Labbadia.
Earlier, Mueller, who has made a name for himself with six goals in all competitions this season, was set up by Italian World Cup winner Luca Toni to put Bayern on the path to victory.
Toni's effort on goal was deflected into the path of Mueller and the midfielder slammed home his shot on 42 minutes as Bayern went fifth, six points behind the leaders.
"In the first half, we controlled the game, but we gave away too much ball," said Bayern boss Louis van Gaal.
"We didn't give them any chances in the second-half and we dominated the game, but the late goal we conceded was unnecessary and angered me. But despite that, I am happy with the win."
Bayern were without their main strike-force of striker Ivica Olic, plus wingers Arjen Robben and Franck Ribery, but Munich made sure of the three points when Freiburg's South Korean defender Du-Ri Cha scored an own goal.
Under pressure from Mueller, Cha attempted to pass back to his goalkeeper, but could only watch as the ball rolled into his own net on 68 minutes.
Freiburg hit a consolation goal in injury time when striker Stefan Reisinger met a cross from striker Mohamadou Idrissou.
Schalke are third after they sealed a 2-1 win over Stuttgart as ex-Germany striker Kevin Kuranyi hit the second-half winner.
Germany's Brazil-born striker Cacau equalised for Stuttgart on 73 minutes after Schalke midfielder Ivan Rakitic had put the Royal Blues ahead in the first-half.
But Kuranyi popped up with the winner in the 76th minute as Schalke claimed their third straight league win.
Werder Bremen are fourth after they sealed a 2-0 win over Hoffenheim with goalkeeper Tim Wiese saving a first-half penalty from Carlos Eduardo after only 14 minutes.
Both goals came just moments later in the first half as Peru striker Claudio Pizarro put his side ahead with a header on 18 minutes before Germany defender Per Mertesacker added a second on 22 minutes.
Cologne picked up three more valuable points to pull away from the bottom three and up to 14th after their 1-0 win at home to Mainz while Eintracht Frankfurt beat Hanover 2-1.
Hertha Berlin remain rooted to the bottom, and are now five points from safety, as they were well-beaten 3-0 at fellow relegation candidates Nuremberg.
On Sunday, defending champions Wolfsburg are at home to Borussia Moenchengladbach while Borussia Dortmund are at home to Bochum.