The German top-flight champion fielded an additional player briefly during last weekend's 4-1 league win, with Kingsley Coman staying on despite Nagelsmann making a double substitution.
Freiburg reluctantly lodged an appeal to the German Football Association (DFB) for its opponent to forfeit the result, but Nagelsmann may have been more preoccupied with a surprise midweek defeat.
Bayern was off the pace at Villarreal in the first leg of its UEFA Champions League quarter-final as it fell to a 1-0 loss, but a positive decision for the Bavarian giant on the DFB's ruling was confirmed on Saturday (AEST).
The league has decided to uphold the original result against Freiburg and the former RB Leizpig coach expressed his satisfaction after seeing the points preserved ahead of Sunday's (AEST) game with Augsburg.
"I'm happy we keep the points," he said. "I think that's quite normal.
"What's important to me [is that] I'm in no way disappointed with Freiburg. The contest against the result has not changed that."
Bayern takes a nine-point lead into its clash at Allianz Arena, but could well be more focused upon the return leg against Unai Emery's Villarreal in Europe.
Nagelsmann, however, says that both games are vital for him, laying out that he intends to rotate his side in order to help his squad find rhythm across two crucial games.
"We have a very important game on Tuesday [Wednesday AEST], probably the most important game of the season," he stated. "But [in] the Bundesliga, we also have to give players some rhythm.
"We will certainly rotate on a few positions. We will let Niklas Sule play from start, we will let [Leon Goretzka] play from the start.
"Alphonso Davies will have a break and [we'll] give a couple [of other] players a little more rhythm for Tuesday [Wednesday AEST].
"It's a very important game for us tomorrow that we are taking very seriously, and are determined and desperate to win."
One man expected to figure will be evergreen playmaker Thomas Muller, with the FIFA World Cup winner in line to feature against Augsburg.
If he does so, and if Bayern is victorious, the 32-year-old will become the first outfield player to amass 300 wins in the Bundesliga.