Bayern stay on course to win the title for a sixth straight season as they leave RB Leipzig behind in second, while Dortmund are now six points off the pace in third.
Having beaten RB Leipzig 5-4 away on penalties when their second-round tie finished 1-1 after extra-time on Wednesday, Bayern have drawn Dortmund in a repeat of last season's semi-final.
Bundesliga: Pressure grows on Werder coach Alexander Nouri after loss to Augsburg; Stuttgart defeat Freiburg
The defeat leaves Freiburg just above the relegation places while Stuttgart are 12th.
Bundesliga: Felix Uduokhai's late strike helps Wolfsburg draw with Hoffenheim; Hertha Berlin held by Freiburg
The late goal cancelled out a penalty by Germany midfielder Kerem Demirbay which had put Hoffenheim ahead.
Bayern head north to Hamburg, who are winless in their last six games, with another big win on the cards.
Bayern Munich will play their first game under returning coach Jupp Heynckes when they host Freiburg this Saturday.
Bayern threw away a two-goal lead for the second league game in a row after being held 2-2 at home to Wolfsburg ten days ago.
As Sagnol takes over for the time being, Bayern will be looking to reboot their season. Here are five things to look out for in the Bundesliga this weekend
Borussia Dortmund set out for Wednesday's Champions League tie against Tottenham Hotspur in London hoping their stars will become "heroes" in a group containing titleholders Real Madrid.
Liverpool winger Ryan Kent says a conversation with Jurgen Klopp and the desire to make the grade in the German league convinced him to take a year's loan-spell at Freiburg.
German Bundesliga leaders Bayern Munich twice surrendered the lead in a 2-2 draw at 10-man Eintracht Frankfurt on Saturday and Borussia Moenchengladbach missed two penalties in a goalless draw against Hamburg SV
The treble winners have 10 points from four games.
Thomas Mueller's first-half penalty and Anatoliy Tymoshchuk's 79th-minute strike gave the Bavarians, who take on champions Borussia Dortmund on Saturday, their 12th win in 14 league matches.