Dortmund headed to the capital looking to build momentum after winning 1-0 against Hoffenheim in their last league game and securing top spot in UEFA Champions League Group D in midweek, but were undone by Schieber, who left Signal-Iduna Park in July.
Schieber, 25, kept his composure to power into the net in the 40th minute after Per Ciljan Skjelbred had dispossessed Jakub Blaszczykowski and slipped him through on goal.
The result keeps Dortmund very much in the mire at the wrong end of the table, although their fans may take some solace from local rivals' Schalke's 2-1 home defeat to Cologne.
Anthony Ujah's 47th-minute strike and a penalty from Matthias Lehmann did the damage for the visitors, with Leroy Sane's late goal proving to be nothing more than a consolation for Roberto Di Matteo's team.
There were no such difficulties for unbeaten Bundesliga leaders Bayern Munich, though, as they produced a scintillating second-half display to seal a 4-0 triumph at Augsburg.
Bayern's four goals came in the space of just 13 minutes, centre-back Mehdi Benatia's 58th-minute opener followed by a double from winger Arjen Robben and a powerful drive from Robert Lewandowski.
The comfortable win means Pep Guardiola's side - who have conceded just three goals in 15 top-flight outings this season - are 10 points clear of second-placed Wolfsburg ahead of their clash with Paderborn on Sunday.
Elsewhere, Davie Selke rescued a 3-3 draw for struggling Werder Bremen versus Hannover, the teenage forward netting two minutes from time after the hosts had thrown away a 2-1 lead.
Saturday's other early fixture saw Freiburg draw 0-0 with Hamburg.
