Dortmund started reasonably well, recycling possession and pushing the hosts back. Sebastian Kehl could not quite convert from a corner while Lukas Kruse beat Marco Reus to the ball when he was played in.
The opener was not long in arriving though just 12 minutes in, Kehl sprayed the ball out for Eric Durm who did well to control and cross for Aubameyang to slot home. Paderborn responded and Roman Weidenfeller did well to deny Süleyman Koç who was put through. Reus then played a clever reverse ball to Aubameyang whose snatched effort went wide.
The fourth official had just put up the board for one minute of stoppage time, at the end of the first half, when Die Schwarzgelben doubled their lead. This time Aubameyang turned provider as he played a brilliant through ball to Reus who calmly tucked the ball away.
The second half had barely started when Kruse saved well from Reus, to keep the home side's slim chances of a result intact. Rupp halved the deficit on the hour mark, sidefooting into the bottom corner from just inside the area after skipping past a desperate tackle.
Another blow shortly followed, when Reus was stretchered off after taking a nasty tackle on his beleagured ankle. Substitute Kevin Großkreutz then had a good chance to give the visitors another two goal-lead but could only poke his effort narrowly past the post. The German international had a goal disallowed for offside.
Paderborn equalised with just under 10 minutes left, former Borussia striker Saglik headed home from a corner to tie the match.