Dortmund went with the tried and tested, as interim manager Edin Terzic looked for a second win in a row following Lucien Favre's dismissal.
Jadon Sancho should've opened the visitors' account ten minutes in from a shot in the centre of the area, but Andreas Luthe came up with a smart save.
Berlin were alive towards the midway period of the first half with Taiwo Awoniyi firing from the near side of the area before Cedric Teuchert blazed a telling ball over the top.
The two sides continued to have a go at each other minutes before halftime through Sheraldo Becker on the side of Berlin whilst Emre Can and Sancho went close for the visitors.
Berlin stunned the Black and Yellow on 57 minutes after Awoniyi propped up in the centre of the six-yard area to send a corner-kick from Grischa Promel into the net.
It would last just three minutes when Youssoufa Moukoko feed off a through ball from Raphael Guerreiro inside the area for an excellent top corner finish.
Dortmund were fired up soon afterwards and could've gone ahead for the first time from an inviting header by Manuel Akanji, but the attempt went wide.
The host restored their earlier advantage 12 minutes from time when Marvin Friedrich charged onto a cross off a corner from Teuchert to head into the bottom corner.
Berlin went close to a third in the closing minutes while Dortmund pushed for a comeback, however the former claimed victory to strengthen their top-four hopes.