The German Football Association (DFB) on Friday rejected Freiburg's appeal following a substitution mixup by Bayern Munich in their Bundesliga match last week, protecting the Bavarians' nine-point lead going into the final six matches.
The Court ruled it was not Bayern's fault that it played with 12 players for several seconds late in the game, but that of the match officials.
Bayern won the game 4-1 but in the 86th minute due to a mixup between club officials and the fourth official during a double substitution, the wrong number for Kingsley Coman was shown on the substitution board.
The winger did not leave the pitch until about 16 seconds later.
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Under German FA rules if a team is found to have introduced a non-eligible player then the opponents are awarded the game by a 2-0 scoreline.
"The DFB sports court has decided that Bayern Munich cannot be blamed for the introduction of a non-eligible player," the DFB said in a statement.
"It is more down to the mistaken behaviour of the officials that a 12th man was introduced and the game continued."
Freiburg can appeal the decision within one working day of its publication.
The decision is a big boost for Bayern, who followed up last week's substitution blunder with their first Champions League loss of the season at Villarreal in midweek.
"I am obviously happy that we get to keep the points (from the Freiburg game)," Bayern coach Julian Nagelsmann told a news conference. "I would also like to make it clear that I am not disappointed at all by Freiburg or coach Christian Streich for (appealing) it."
Nagelsmann had said he would not have appealed the result given that there was no impact on the game itself.
The Bavarians, on course for a record 10th straight league crown, is on 66 points with Borussia Dortmund in second place on 57. Dortmund is in action at VfB Stuttgart on Friday before Bayern take on Augsburg a day later.
Freiburg, battling for a Champions League spot, remain in fifth place on 45.