Christopher Nkunku, Alexander Sorloth and Emil Forsberg scored the goals in Freiburg, which lifted Leipzig one point ahead of Bayern, but the Munich men moved back to the top of the table later in the day after a 4-2 win against Borussia Dortmund at Allianz Stadium.
Leipzig impressed in its final tune-up before facing Liverpool in Budapest next Thursday (AEDT) in the Round of 16 of the UEFA Champions League having lost the first leg 2-0.
Leipzig took the lead at Freiburg after a first-half blunder by home goalkeeper Florian Mueller.
His loose pass from the back was snapped up by Leipzig striker Yussuf Poulsen, who squared for French winger Nkunku to tap home four minutes before the break.
Sorloth continued his great form and midway through the second half he converted Nkunku's assist.
The Norwegian, who scored the last-gasp winner over Moenchengladbach a week ago, then set up Forsberg who banged in Leipzig's third goal 11 minutes from time.
Elsewhere, third-placed Wolfsburg is now eight points adrift of Leipzig having stumbled to a 2-1 defeat at mid-table Hoffenheim, whose striker Andrej Kramaric scored the winner just before half-time.
Eintracht Frankfurt stays fourth after Filip Kostic equalised for the home team in a 1-1 draw against Stuttgart.
A late goal by Bayer Leverkusen striker Patrik Schick sealed a 1-0 win at Borussia Moenchengladbach, which drops to 10th as its miserable run continues.
Gladbach has now lost all fives games since it was announced head coach Marco Rose will take charge of Dortmund next season.
"The fun and joy is missing in our football," Gladbach midfielder Hannes Wolf admitted.
The away win eases the pressure on Leverkusen coach Peter Bosz.
His fifth-placed side had failed to win any of its five previous games in all competitions.
Dodi Lukebakio converted a late penalty to seal Hertha Berlin's 2-1 home win over Augsburg.
It was Hertha's first victory in 10 games which pulled it up to 14th and away from the relegation fight.
Coach Pal Dardai described the win as a "magic moment" as he enjoyed his first victory since replacing Bruno Labbadia at Hertha in January.