Lucas Barrios put Dortmund ahead five minutes before the break and an own goal from Ralph Gunesch early in the second half wrapped up the points for Jurgen Klopp's men.
The Westphalians could, and probably should, have won by a more comfortable margin but missed several chances as St Pauli crashed to their first defeat of 2011 without showing much resistance.
Dortmund made it clear from the whistle that they wanted the points, putting St Pauli immediately under pressure with Kevin Grosskreutz the first to test Thomas Kessler in the second minute.
The hosts continued to create openings, but lacked the final touch to transform their dominance into goals.
Both Mario Gotze and Marcel Schmelzer managed to get in around the back of the St Pauli defence, but neither found takers for their passes into the middle.
Kessler then denied Nuri Sahin, who tried his luck from more than 30 yards out on the half hour mark, as Dortmund got closer to opening the scoring.
Their first goal came in the 39th minute when Sahin's cross was brought down well inside the area, and he turned and placed his shot into the bottom right-hand corner.
They doubled their advantage four minutes into the second half when Gunesch unfortunately turned Barrios' low cross into his own goal.
Dortmund continued to dominate the play with Barrios and Robert Lewandowski both missing good chances before substitute Antonio da Silva's shot was diverted behind by Kessler.