Champions Bayern Munich climbed into second place for the first time this season with a comfortable 3-1 win at Mainz 05.
The league's top scorer Mario Gomez notched his 18th goal of the season to help seal Bayern's sixth win in eight matches.
Dortmund's Lucas Barrios scored his 10th league goal of the campaign in the first half and an own goal from Ralph Gunesch just after the restart gave the hosts, who drew their two previous matches, a points total of 55.
"This was a well-deserved win because our discussions about converting our chances paid off," said Dortmund coach Jurgen Klopp. "The team remained concentrated and focused on their aim."
Klopp's side will need to maintain that focus when they take on resurgent Bayern next week.
Hanover 96 beat Kaiserslautern 3-0, thanks to a double from Jan Schlaudraff, to stay fourth on 41 points.
Paolo Guerrero also struck twice as Hamburg SV crushed Werder Bremen 4-0 in the northern derby to leave their rivals without a win in five games and only a point off the relegation play-off spot.
The win gave Hamburg, who left unhappy striker Ruud van Nistelrooy on the bench, some respite following their midweek defeat by bitter city rivals St Pauli and increased the pressure on Werder coach Thomas Schaaf who has been at the club for 12 years.
VfL Wolfsburg slumped to their second straight defeat under new coach Pierre Littbarski, letting slip a 1-0 lead to lose 2-1 at Freiburg.
EXPLOSIVE START
Dortmund made an explosive start against St Pauli as Kevin Grosskreutz was denied by keeper Thomas Kessler and Nuri Sahin fired just wide from 16 metres in the opening minutes.
St Pauli, who won three games in a row going into the match, were helpless as Dortmund launched wave after wave of attacks.
Kessler made several more fine saves but had no chance when Paraguay international Barrios turned on the style six minutes before the break.
He picked up a deep cross from Sahin, turned in the box, laid the ball on to his left foot and fired in.
Dortmund struck again in the 49th minute when the ball bounced in off Gunesch's leg.
