كتب : Hatem Maher
The German international's goal one minute from time cancelled out a second-half striker from Thomas Brdaric.
The draw maintained Bayern's position on the top of league table with 55 points while Hannover lie fifth on 30 points.
Brdaric put Hannover ahead in the 55th minute against the run of play after meeting a cross with a backward header past Bayern keeper Michael Rensing, who came as a substitute to injured Oliver Kahn.
Germany captain Ballack secured his side a point before the final whistle when he connected with a perfect-inch cross to head home.
Elsewhere, Ivan Klasnic struck in the 37th minute to lead Werder Bremen to a 1-0 away win over Borussia Dortmund.
Bremen narrowed the gap with leaders Bayern to nine points as they are in second place with 46 points.
In other matches, Bayer Leverkusen beat Duisburg 3-2, Borussia Monchengladbach defeated Cologne 2-0, Kaiserslautern edged Arminia Bielefeld 2-0, Schalke cruised past Hertha Berlin 2-1 and Nurnberg downed Wolfsburg 1-0.