The visitors started brightly, with Admir Mehmedi having an effort saved as early as the second minute.
Makoto Hasebe then came close to breaking the deadlock but his low drive from outside the box was well kept out.
Both sides had half-chances, but neither was able to break the deadlock in a goalless first half, before Freiburg came out much the stronger team.
In the 70th minute Oliver Sorg was handed his second yellow card and sent off, but it was his team that got the crucial second goal.
Vladimir Darida latched on to a headed pass from Francis Coquelin to rifle into the top corner from distance before the points were secured by Mehmedi late on.