It took 15 minutes for Freiburg to open the scoring against a side who are still not sure of survival themselves, as Schuster fired in from 25 yards after collecting a pass from Vladimir Darida.
Mehmedi then had a hand in two goals within the space of six minutes after the interval as Freiburg extended their advantage. He squared for Klaus to convert his fourth goal of the season on 53 minutes.
Swiss striker Mehmedi then added his own name to the scoresheet before the hour mark, pouncing on the rebound of Klaus's shot to see the hosts beat Raphael Wolf for the third time in the evening.
Reported Tottenham Hotspur and Southampton target Aaron Hunt assisted Petersen on 70 minutes as Bremen pulled one back, but it was not enough for them to continue their five-match unbeaten run.
Freiburg are now four points clear of the Bundesliga relegation zone, and four behind Werder in the table.