The first meeting of the bitter rivals in seven years, following Hamburg's relegation to the second division last season, was watched by a capacity 57,000 crowd at their Volksparkstadion stadium.
The build-up had been overshadowed by clashes and tension between rival fan groups, but the match day proved quieter than feared with only a handful of minor incidents off the pitch.
Hamburg police deployed 1,500 officers in the northern city, and set up a webpage on which witnesses could report disturbances.
Many St. Pauli fans had to cover their noses as they arrived at the stadium in specially organised S-Bahn trains.
The night before the game, foul-smelling butyric acid had been spread at the Bahrenfeld S-Bahn station on the away fans' route, police confirmed to Bild newspaper.
There were also reports of similar stink bombs in the away block itself, while local newspaper Hamburger Morgenpost reported that excrement had been spread on the floor near the away fans' entrance.
The St Pauli fans also set off a number of flares ahead of kick-off, but there were fewer fireworks on the pitch.
Hee-chan Hwang and Douglas Santos came close for Hamburg in the second half, while St. Pauli's Cenk Sahin forced a scrambling save from Julian Pollersbeck in stoppage time, but neither side was able to break the derby deadlock.
The point left Hamburg third in the division while St Pauli are sixth.