Augsburg managed to equalise three times before Gio Reyna's 78th minute looping shot gave the hosts victory in their season restart following a two-month break.
Dortmund, who saw Ivory Coast forward Haller come on as a second-half substitute for his first appearance after his surgeries and therapy for testicular cancer since July, are sixth on 28 points.
Dortmund struck after 29 minutes with Jude Bellingham weaving a shot through three defenders after creating just the bit of space he needed with a superb move.
The Dortmund defender, however, made amends only two minutes later, heading in from a free kick to put them back in front.
Dortmund coach Edin Terzic brought on Haller and Jamie Bynoe-Gittens to add more punch to his attack and it paid off with the latter thundering in their third goal from outside the box in the 75th.
But Dortmund's leaking defence again failed to hold on to the lead with Augsburg's substitute David Colina tapping in off the rebound after fellow sub Kelvin Yeboah's shot had bounced off the post just two minutes later.
The visitors, however, had run out of ideas after Reyna's shot in the 78th from just inside the box put Dortmund back in the driver's seat for a fourth time.