Having beat 2-1 in the fourth round of the Champions League, Roedehausen of the German Cup on Tuesday, Bayern have again returned to the Allianz Arena, one week before facing Borussia Dortmund. .
"This week we did not show our best football, when that happens, things are not coming easily," said Bayern captain Manuel Neuer.
This was the first time Freiburg left Munich for a point since 1997.
The Bayern Munich striker needed 80 minutes to give the winner a penalty when Serge Gnabry fired the defender and hit the corner.
However, Freiburg showed confidence after Lucas Hoeler was involved in Bayern's Niklas Suele and Jerome Boateng to equalize in the 89th minute and leave Bayern Munich's Niko Kovac.
"It would be a bit easier if Lewy (Robert Lewandowski) had a chance," said Kovac after Lewandowski missed several chances.
"The second half was fantastic, we were disappointed."
There are bad news from Kovac as Borussia Moenchengladbach can return to the final of Bayern with a point from Fortuna Duesseldorf.
Dortmund are back in the top four in the Bundesliga with a 1-0 win over Wolfsburg as Marco Reus headed the lead in the first goal.
Lukasz Piszczek and Marcel Schmelzer mean Borussia Dortmund are trying to defend their defense and struggling to complete their chances.
England winger Jadon Sancho, 18, has already scored six goals in the league this season, with Thomas Boateng firing back from Reus, who took the ball 28 minutes from time.
It was the 30th goal of the season in Dortmund's only 10 league games, but it was far from the impressive form of leaders.
Borussia Dortmund's Paco Alcacer, whose first-team debut has failed to reach his side after scoring seven goals in his first four Bundesliga games.
Nelson goes through fuel
After winning two successive wins in Bayer Leverkusen's 6-2 win over Werder Bremen last Sunday with a 5-0 win over Borussia Moenchengladbach in midweek, Hoffenheim beat 4-1 at home to Joelinton with a double goal.
The son of Reiss Nelson, on loan from Arsenal, has once again fired on the right wing, with the 18-year-old netted his fifth goal in six Bundesliga games this season.
Leverkusen winger Karim Bellarabi has sent Germany coach Joachim Loew to his marking goal. Loew has named his name in Russia and Netherlands next week.
However, the scores were only four minutes long.
Joelinton gave Hoffenheim the lead and then won the penalty, and Vincenzo Grifo equalized for Italy in the 49th minute.
Joelinton scored the last 17 minutes for the visitors at Grifo, leaving them pushing for Leverkusen's Heiko Herrlich.
Meanwhile, Schalke are preparing for Tuesday's Champions League clash against Galatasaray with a 3-1 win over Hanover with goals from Nabil Bentelab, Mark Uth and Breel Embolo.
Uth, who had a penalty clear before the break, won the free kick for Bentaleb after the game, after he scored 85 minutes from his first goal for Schalke since the summer Hoffenheim.
It finished 2-2 Augsburg Bavarian wall as Nurnemberg victims hit a point.