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.
Coach Jupp Heynckes told reporters that Ballack, substituted in the 6-3 home defeat by Borussia Moenchengladbach in his previous outing, had suffered an injury to his left knee and would undergo a scan.
"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.
Didier Ya Konan and Mohammed Abdelloue had put Hanover 2-0 ahead, despite a red card for Emanuel Pogatetz before half-time.
Greek forward Theofanis Gekas, who last week announced his international retirement, scored twice to help Eintracht Frankfurt win 4-0 at erratic Moenchengladbach.
Benjamin Koehler and Patrick Ochs scored the other goals as Eintracht picked up their first points of the season.
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.
Freiburg came behind to beat VfB Stuttgart 2-1, leaving their opponents pointless and bottom of the table after selling midfielder Sami Khedira to Real Madrid in the close season.
Hoffenheim, 2-0 winners over Schalke 04 on Friday, lead the table with nine points.
DZEKO CLOSE
Wolfsburg nearly took a first-half lead when Edin Dzeko, last year's Bundesliga topscorer, rattled the crossbar from 30 metres.
But they were lucky to reach the break with 11 men when Brazilian midfielder Diego escaped a red card for petulantly kicking an opponent from behind.
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.
