A goal from Kevin Grosskreutz in the 66th 0, at the Olympiastadion.
The loss is the fifth straight for Hertha, which sits two points above the drop zone, and will be taken over by new manager Otto Rehhagel following the dismissal of Michael Skibbe last weekend.
Despite the loss Hertha will be encouraged by the fact that they missed a number of chances against Dortmund and could very well have claimed a point from the game.
Raffael forced Dortmund goalkeeper Roman Weidenfeller into action before the break, while Patrick Ebert just missed putting Hertha in front early in the second half.
But Dortmund snatched the lead when Robert Lewandowski's header was pushed onto the crossbar by goalkeeper Thomas Kraft, who was unable to keep out an overhead kick from Grosskreutz.
The win moves Dortmund three points clear at the top of the league.
Freiburg 0, Bayern Munich 0
Bayern beat the home side 7-0 at the Allianz Arena earlier this season, but Saturday proved to be a different story as Freiburg created as many chances as the visitors and had the best opportunity to win the game in the final 10 minutes.
Holger Badstuber had the ball in the net for Bayern after eight minutes but the goal was called back for offsides.
Bayern brought Arjen Robben on at halftime and he tested goalkeeper Oliver Baumann early in the second half, but the hosts defended well and almost grabbed the win in the 84th minute when Daniel Caligiuri forced a save from Bayern goalkeeper Manuel Neuer at his near post.
Monchengladbach 2, Kaiserslautern 1
Kaiserslautern, Germany - Kaiserslautern's relegation fears deepened on Saturday after Monchengladbach came to the Fritz-Walter-Stadion and emerged as 2-1 winners.
The visitors jumped out to a 2-0 lead inside of 15 minutes with goals from Patrick Herrmann and Juan Arango before Kaiserslautern began to mount a comeback.
A long-range effort from Leon Jessen cut the deficit to 2-1 with 25 minutes still to play, but after substitute Dorge Kouemaha went close for the hosts, they were unable to produce a second goal and have gone winless in 12 straight games.
Monchengladbach has won five of its last six to move past Bayern Munich and into second place.
Bayer Leverkusen 4, Augsburg 1
Leverkusen, Germany - Bayer Leverkusen bounced back from a midweek defeat in the Champions League to claim a 4-1 victory at home against relegation- battling Augsburg.
Leverkusen was beaten 3-1 at the BayArena by Barcelona on Tuesday, but got off to a positive start with Stefan Kiessling heading home the first of his two goals in the 25th minute.
Augsburg leveled the match through Koo Ja-Cheol shortly after halftime, but Gonzalo Castro restored Leverkusen's advantage 10 minutes later by scoring from a few yards out.
Kiessling added to the lead a few minutes later after being set up by Andre Schurrle, who put his name on the scoresheet in the 70th minute after Kiessling returned the favor.
Werder Bremen 3, Hamburg 1
Hamburg, Germany - Werder Bremen snapped a string of four successive draws on Saturday by posting a 3-1 win over Hamburg at the HSH Nordbank Arena.
Marko Marin's early strike put Bremen in front before a goal from Tom Trybull just before halftime doubled the advantage.
A free kick from Hamburg's Mladen Petric made its way through the wall and took a deflection on its way past goalkeeper Tim Wiese, reducing the deficit to 2-1 with 15 minutes to play.
But Bremen put the result out of reach in the 86th when Marko Arnautovic latched on to a long clearance by Wiese to notch his sixth goal of the campaign, keeping the visitors in possession of fifth place.
Nurnberg 2, Cologne 1
Nurnberg, Germany - Cologne sustained its fifth loss in six games on Saturday as Tomas Pekhart's goal five minutes from time handed Nurnberg a 2-1 home win.
Alexander Esswein fired Nurnberg in front in the first half when he scored from the edge of the penalty area, but his opener was canceled out in the 66th minute by Milivoje Novakovic, who netted his third goal of the season after being set up by Odise Roshi.
Esswein not only scored the first goal for Nurnberg but he set up the winner five minutes from time when his cross was headed home from the middle of the penalty area by Pekhart, handing Nurnberg three points to move the club seven above the drop zone.