First-half goals from Christian Guenter and Janik Haberer and a third on the hour by Nils Petersen gave Christian Streich's team a deserved victory and maintained their fine start to the season.
Freiburg are in third place on nine points, one ahead of champions Bayern Munich, who drew 1-1 at RB Leipzig on Saturday.
Schalke 04 fired five goals past hosts Paderborn after falling a goal behind to earn their second straight win.
Cauly put the hosts ahead but the Royal Blues roared back with goals from Salif Sane and Suat Serdar.
Amine Harit then scored either side of an Ahmed Kutucu goal to make it 5-1 as Schalke climbed to seven points.
Leipzig lead the standings on 10, with Borussia Dortmund in second on nine, ahead of Freiburg on goal difference.