The hosts were in control for most of the match but failed to get the better of visiting goalkeeper Philipp Tschauner to gain their first win of the season.
Köln boss Holger Stanislawski, up against the club served for 18 years as both player and coach, made five changes to his starting line-up in an effort to kick-start their season. His St. Pauli counterpart Andre Schubert left his side unaltered after beating SV Sandhausen on Matchday 4.
The home team went on the offensive right from the off and attacking midfielder Sascha Bigalke was particularly influential in the opening stages, testing Philipp Tschauner twice in quick succession, but was unable to convert either chance.
Köln on top
Köln continued to press as St. Pauli sat deep, with clear-cut opportunities few and far between until Thomas Bröker, scorer of Köln's only goal so far this season, went close with a fierce drive in the 35th minute. St. Pauli did not not respond until the shortly before half-time, when Fabian Boll's attempt after a good run from Mahir Saglik was saved by Timo Horn.
It was a similar story in the first minutes of the second half, with the Billy Goats continuing to push for the first goal. Adel Chihi should have done better from close range but his shot was easily saved by Tschauner, while Bröker fired just wide from an acute angle only two minutes later.
St. Pauli started offering a little more in attack just before the hour mark when midfielder Fin Bartels twice went close but he could not find a way past 19-year-old Horn. Mahir Saglik squandered St. Pauli's best opportunity in the 73rd minute, but he fired his volley straight at the Köln shot stopper.
In the closing stages both sides had chances to snatch victory, but poor finishing ensured the match finished goalless. Köln remain in the bottom three on two points, with St. Pauli four points better off in eleventh.