Emmanuel Dennis scored his first goal in Germany and fellow Nigerian, Tolu Arokodare, was also on target in the penalty shootout, but FC Cologne will eventually crash out of the Cup in Germany at lower league side SSV Jahn 2000 Regensburg.
Bundesliga 2 side Jahn 2000 Regensburg advanced to the fourth round of the cup in Germany after they won 4-3 on penalties as the teams played out a 2-2 draw even after extra time.
Dennis, who is on loan from Belgian champions Club Brugge, justified his first start with a goal in the 22nd minute for Cologne to race into a 2-0 lead, before their opponents fought back to draw level before halftime.
The forward, who made his Cologne debut on Monday in a 3-1 home win over Arminia Bielefeld, scored another goal on 78 minutes, but it was chalked off.
He was replaced by Arokodare in the 96th minute and the young striker scored during the penalty shootout.