German star Marco Reus gave Dortmund an early lead before Gabon winger Aubemayang added two second-half goals in Borussia's first win since the start of December.
Dortmund now face mid-table Mainz and strugglers Stuttgart in the league before Italian league leaders Juventus away in the last 16 of the Champions League on February 24th.
"We must keep believing things will move forward after three or four months in which they didn't. Today was a step in the right direction," said relieved Dortmund coach Jürgen Klopp.
The result lifted Dortmund to 16th, while Freiburg slip to 17th, still leaving both teams in the drop zone with Borrusia out to avoid their first relegation since 1972.
Freiburg got off to the worst possible start when midfielder Mike Frantz played a poor back pass which was snapped up by Aubemayang.
The fleet-footed winger drew Freiburg goalkeeper Roman Buerki and squared for Reus to tap into an empty net with nine minutes gone.
Aubemayang then darted onto Ilkay Gundogan's superb through ball and planted his shot past Buerki on 56 minutes.
His second followed on 72 minutes when he fired home after some superb passing from Dortmund's midfield trio of Reus, Shinji Kagawa and Jakob Blaczszykowski.
Leaders Bayern Munich continued their march to a third straight title with a 2-0 win at VfB Stuttgart, which saw Huub Stevens' side drop to bottom of the table.
"It was very important to score just before half-time. I'm happy for both myself and the team – it was important to get a win today," said Bayern goal-scorer Arjen Robben.
Bayern's win was their first in three matches having been thrashed 4-1 at Wolfsburg just over a week ago.
Robben scored his second goal in as many games when he fired home from 13 metres out just before the half-time break to give Pep Guardiola's side the lead.
Left-back David Alaba then drilled home a superb free-kick from 30 metres out to make it 2-0 with 50 minutes gone.
Bayern stay eight points clear of second-placed Wolfsburg who gave Germany
winger Andre Schuerrle his debut after he moved from Chelsea in a 3-0 win at
home to Hoffenheim.
Belgium midfielder Kevin de Bruyne claimed two goals in the impressive
Schuerrle needed just three minutes to make his mark when his pin-point
accurate cross was met by Bas Dost for the Dutch striker to fire home his
fourth goal in four games.
Schuerrle clattered the crossbar with a shot on 28 minutes, but De Bruyne
headed home the rebound.
Dost then turned provider for De Bruyne to claim his eighth goal of the
season — his fifth in the last three games — in what is proving a productive
campaign for the 23-year-old.
Hertha Berlin bounced back from the sacking of coach Jos Luhukay on
Thursday with an impressive display which lifted them out of the bottom three
after their 2-0 win at ten-man Mainz 05.
With Hungary national team coach Pal Dardai now at the helm, the visitors
took the lead when Jens Hegler netted a 35th-minute penalty after former
Manchester City goalkeeper Loris Karius was sent off.
Hertha doubled their lead on 43 minutes when Roy Beerens slotted home after
Valentin Stocker had hit the post to leave Berlin 14th.
Hamburg continued their march up the table to go 11th after their second
consecutive victory with a 2-1 win at home to Hanover 96.
Hanover's Brazilian defender Marcelo gave Hamburg the lead when he turned
the ball into his own net after 26 minutes.
Ex-Germany midfielder Marcell Jansen added Hamburg's second on 50 minutes
before Poland striker Artur Sobiech scored Hanover's consolation with just
over 20 minutes left.
Hanover are eighth despite being winless in their last four games.
Paderborn dropped to just above the relegation spots after their goalless
draw at Cologne while Schalke 04 went third on Friday with a 1-0 home win
against Borussia Moenchengladbach.