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With Dortmund beating Hamburg 2-0 on Friday to open a seven-point lead at the top of the table, Leverkusen are now level on 24 points with second-placed Mainz, but go third on goal difference. Mainz play Hanover on Saturday evening.
After a frustrating afternoon in Hamburg, Leverkusen got the break they needed when Germany midfielder Simon Rolfes beat the defence and squared for Renato Augusto to net in the 81st minute.
"We could have been 3-0 up at half-time and we knew things would be hard for us," said Leverkusen coach Jupp Heynckes.
"St Pauli had rolled up their sleeves and caught us cold.
"But my side showed they have bulletproof spirit and earned the win."
Moenchengladbach got themselves off the bottom of the Bundesliga with an impressive 4-0 win over Cologne.
After last Saturday's 3-3 draw at Bayern Munich, 'Gladbach picked up only their second win of the season to put Cologne bottom of the table.
Schalke claimed a point as they fought back from 2-0 down to draw at Wolfsburg after strikers Edin Dzeko and Grafite both scored for the hosts.
With the Wolves cruising at 2-0 with half an hour played, Schalke hit back with goals by Brazil striker Edu on 39 minutes and Dutch striker Klaas Jan Huntelaar scored his seventh goal of the season to equalise in the second-half.
The result leaves Schalke 16th and Wolfsburg in 12th.
Stuttgart allowed a 3-0 lead to slip to a 3-3 draw at Kaiserslautern.
Ivory Coast defender Arthur Boka opened the scoring after just 19 minutes before Germany internationals Cacau and Christian Gentner, with a penalty, put Stuttgart 3-0 after 50 minutes before the hosts hit back.
Bulgaria international Ilijan Micanski netted on 58 minutes before Croatian midfielder Ivo Ilicevic smashed home his shot from the edge of the penalty area on 74 minutes to set up a tense finish.
Defender Mathias Abel scored the equaliser with a header on 78 minutes to complete the comeback and share the points.
The draw lifts Stuttgart to 14th and puts Kaiserslautern 15th while Werder Bremen remain in midtable after their goalless draw with Eintracht Frankfurt.
On Friday, Bundesliga leaders Dortmund underlined their credentials at the top of the table with a 2-0 home win over Hamburg in the rain to open a seven-point lead with second-placed Mainz playing Hanover on Saturday evening.
In pouring rain at Dortmund's packed Signal Iduna Park in front of a sell-out 80,720 crowd, second-half goals by Japanese midfielder Shinji Kagawa, his sixth of the season, and Lucas Barrios, his seventh, sealed the win.