Cedric Makiadi gave Freiburg the lead against the run of play after half an hour when he forced the ball over the line after Jonathan Schmid's shot was parried by Augsburg goalkeeper Alexander Manninger.
Max Kruse set up the second for the team from the Black Forest region as he split the Augsburg defence with a clever through ball for Schimd and the Frenchman gave Manninger no chance with his finish.
Freiburg stayed an impressive sixth with 48 points from 32 games, which would earn them a place in the Europa League next season. The still have a mathematical chance of qualifying for the Champions League playoff round as they are four points behind fourth-placed Schalke 04 with two games to play.
Augsburg, who had won five of their previous eight games, are 16th, the relegation playoff place. They have 30 points, behind Fortuna Duesseldorf on goal difference.
Hamburg SV, seventh with 45 points, were held 1-1 at home by VfL Wolfsburg in the day's other game, a midtable clash.
Heiko Westermann headed Hamburg in front on the stroke of halftime but the inconsistent hosts were pegged back by Makoto Hasebe's header midway through the second half.