Wolfsburg drew level 11 minutes later when Maximilian Arnold's pinpoint free kick sailed past Timo Horn but Ondrej Duda restored Cologne's advantage in the 43rd, firing a first-time effort into the top corner after neat wing play from Elvis Rexhbecaj.
Cologne's lead was short-lived as Wout Weghorst towered over Sava Cestic to meet Renato Steffen's cross in the 47th minute for his seventh league goal of the season. Wolfsburg laid siege to the Cologne goal in search of a late winner but were unable to test Horn.
The result means Wolfsburg remain in fifth on 18 points, four points behind leaders Bayern Munich who were facing Leipzig later on Saturday. Cologne stay in 15th with seven points from 10 games.