The hosts started slowly with Die Roten looking more confident in possession. But that started to change 11 minutes in when Henrikh Mkhitaryan hit a sweet left-footed half volley on the turn producing an excellent fingertip stop from Ron-Robert Zieler.
That was soon followed by a towering Mats Hummels header from Marco Reus’s corner which was somehow parried onto the crossbar by the excellent Zieler.
After that, Hannover managed to get on the ball more again to stem the pressure and defended the rest of the half out.
Just minutes into the second half, Reus was put through on the left side of the box but his snatched finish was unlike him.
Things got a bit heated when Mkhitaryan was grabbed by Ceyhen Gülselam and the Armenian reacted angrily; both players were booked.
Another great chance for Reus when Lukasz Piszczek pulled the ball back for Pierre-Emerick Aubameyang who laid it off to the German winger but his fellow countryman did well to tip it wide.
Just after the half hour mark, the deadlock was broken against the run of play, Kiyotake curled in a freekick from 25-yards out after a foul from Gundogan.
Kiyotake nearly had a second but his close-range volley was brilliantly saved by Weidenfeller, who denied Joselu just seconds later.
The home side nearly equalised when Eric Durm’s cross was met by a diving Adrian Ramos but his header flashed wide.
Gülselam was sent off after picking up his second yellow when he took out Reus in the 89th minute, however the visitors held on for a memorable win.