However, there wasn't much to indicate that the visitors would escape Viborg with a win in the opening stages of the match, when Viborg took the lead after 24 minutes as Jeppe Gronning converted a penalty after Thomas Delaney had blocked a close-range attempt from Asger Beck with his elbow.
The Danish champions didn't waste much time to recover from the early shock, when the former Viborg-player Elias Aschouri restored parity after 37 minutes, when he found the back of the net after initially hitting the woodwork after a superp breakthrough on the wing.
Six minutes after the restart Mohamed Elyounoussi gave the visitors the lead, when he outjumped Viborg-keeper Stipe Radic to steer home a fine delivery from Mexican defender Rodrigo Huescas.
Jakob Neestrup's side from then on seemed in solid control but the hosts never caved in and brought the home crowd back on their feet after 73 minutes, when Gronning flicked a corner on for Mads Sondergaard who steered the ball into the net from close-range against a helpless Dominik Kotarski.
FC Copenhagen, however had the last laugh, when Magnus Matsson converted a penalty 12 minutes from the end after Jean-Manuel Mbom had brought him down with a rather clumsy challenge.
Victor Froholdt was denied by the woodwork in the closing stages but 3-2 was also enough for the visitors to secure the three points.