Champions Bayern Munich, who have made an unconvincing start to the season with four points from three games and only two goals scored, were held 0-0 at home by injury-hit Werder Bremen in a meeting of two Champions League representatives.
Second-half goals from Dortmund's Nuri Sahin and Shinji Kagawa left 2008-09 champions Wolfsburg without a point after three outings under the former England manager who last year led Twente Enschede to the Dutch title.
Germany captain Ballack, who missed the World Cup through injury, continued his unhappy start to the season when he limped off after just over half an hour of Leverkusen's match following a collision with an opponent.
"It's most probably with the interior ligament," Heynckes told reporters. "We hope that it's not too serious."
Goals in the last 30 minutes from Eren Derdiyok and Patrick Helmes earned a draw for Leverkusen, who have four points, and ended Hanover's 100 percent record.
Hamburg SV dropped their first points when they conceded a late equaliser in a 1-1 draw at home to Nuremberg, Javier Pinola converting an 82nd minute penalty to cancel out Dutchman Joris Mathijsen's goal just after the hour.
Wolfsburg nearly took a first-half lead when Edin Dzeko, last year's Bundesliga topscorer, rattled the crossbar from 30 metres.
Turkey midfielder Sahin broke the deadlock with a curling 30-metre shot five minutes after the break and Japan's Kagawa finished off an incisive passing move for the second to leave Dortmund with six points.
Werder were missing Claudio Pizarro, Per Mertesacker and Naldo for their trip to Bayern but more than held their own and nearly snatched a late win when Hugo Almeida's shot was turned away by Joerg Butt.
