The visitors made the brighter start of the two sides, with Tomas Pekhart going close with a header from close range after just two minutes.
Freiburg, though, took their chance in the 36th minute to go ahead in front of their own supporters when Cedric Makiadi headed home from just yards out.
Pekhart had his effort in the 38th minute from a Kiyotake cross saved by Oliver Baumann in the Freiburg goal.
Kiyotake himself had a chance on the stroke of half-time, but he was denied by Baumann.
Jendrisek tested the Nurnberg goalkeeper again in the 52nd minute when he shot Jonathan Schmid's cross on target.
Freiburg eventually scored their second goal of the afternoon in the second minute of injury time from the penalty spot.
A minute later Freiburg scored their third goal of the match when Makiadi teed up Marco Terrazzino for a fierce shot into the Nuremberg goal from outside the box.