Champions Bayern won 1-0 at home to Freiburg thanks to Xherdan Shaqiri's 35th-minute effort.
The Bavarians rested the likes of Manuel Neuer, Philipp Lahm, Bastian Schweinsteiger and Thomas Muller, with Jerome Boateng the only starter remaining from the 4-0 demolition of Barcelona.
Freiburg's defeat denied them the chance to move about Schalke, who play on Sunday, and into fourth place.
Dortmund left, among others, midweek's four-goal hero Robert Lewandowski on the bench until the 69th minute ahead of their trip to Real Madrid, but still won 2-1 at Fortuna Dusseldorf.
Nuri Sahin opened the scoring after 20 minutes and Jakub Blaszczykowski made it two in the 70th minute, one minute after coming on.
Adam Bodzek got a consolation for the hosts two minutes from time.
Defeat plunged Fortuna back into relegation trouble as the two sides below them both picked up important wins.
Third-bottom Augsburg, in the relegation play-off place, moved level on points with Fortuna thanks to a 3-0 win at home to Stuttgart.
Sascha Molders broke the deadlock in the 61st minute before late strikes from Marcel de Jong and Ji Dong-won sealed the win.
Second-bottom Hoffenheim went to within three points of safety with three games to go with a 2-1 win at home to Nurnberg.
Two goals in the opening 19 minutes from Tobias Weis and Sejad Salihovic put the hosts in control, with Timmy Simons pulling one back from the spot after the break.
Elsewhere, third-placed Bayer Leverkusen win 1-0 at home to Werder Bremen thanks to Stefan Kiessling's 35th-minute penalty.
Wolfsburg beat Borussia Monchengladbach 3-1, Diego scoring one and setting up the other two.
Maximilian Arnold opened the scoring for Wolfsburg in the 34th minute, but
Peniel Mlapa equalised soon after the break.
Ivica Olic put Wolfsburg back in the lead in the 61st minute and Diego finished the match with his strike in the 75th minute.