Bayern, who have now kept a clean sheet in 11 consecutive games, opened up a three-point lead at the top of the table.
Hoffenheim kept the Bavarians, who looked sluggish following their 2-0 win over Manchester City in the Champions League in midweek, in check and twice went close to securing a surprise win through Ryan Babel.
"We had a huge match on Tuesday and we have worked a lot in recent weeks," Bayern coach Jupp Heynckes told reporters.
"We can live with this result. You could feel today the players were not really that fresh," said Heynckes who did not start Arjen Robben after the Dutch winger told him he was not fully recovered from injury.
"If he had felt fit he would have played from the start. It was a joint decision."
Dortmund keeper Roman Weidenfeller made a spectacular save from Sankoh's penalty just after the restart before a charging Mario Gotze latched on to a Lewandowski pass and flicked the ball over the visiting keeper for the third.
Earlier, Wolfsburg's Mario Mandzukic beat his marker in the air to head the equaliser after Gonzalo Castro had given the hosts a first-half lead.
Hertha Berlin climbed to ninth after ending Cologne's short two-game winning streak with a 3-0 victory.
