A 20th-minute goal from Gonzalo Castro and two late goals from Marco Reus and Henrikh Mkhitaryan propelled Dortmund into their third successive Cup final, and they will be hoping it is third time lucky after they finished second best in 2014 and 2015.
Their win also spoiled the hosts' hopes of a home game in Berlin's Olympic stadium on May 21.
Bayern, who overcame Dortmund to clinch the 2014 title, beat Werder Bremen 2-0 on Tuesday to book their ticket to the season finale and a third showdown in the last five editions against Dortmund.
Castro profited from a loose ball to drill in from 20 metres for a deserved Dortmund lead with Hertha happy to just pull back and defend.
Dortmund, who lost 4-3 to Liverpool in the Europa League last eight earlier this month, tried to get another goal in a one-sided first half but were not decisive enough.
Hertha striker Salomon Kalou had two good chances, including a 74th minute header, to punish the visitors for their wastefulness but Reus killed off any chances of a comeback in the very next attack with a shot from inside the box after defender John Anthony Brooks slipped.
Reus then turned provider to set up Mkhitaryan seven minutes from time to score the third goal for the Ruhr Valley club, who are in second place in the Bundesliga. They are seven points behind Bayern with four games left to play.
(Reporting by Karolos Grohmann, editing by Pritha Sarkar)
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