Balotelli converted a 90th-minute spot kick to earn City a lifeline in the competition against an impressive Dortmund side who dominated for large periods and were only prevented from winning the match comfortably by the brilliance of Hart.
The England keeper was beaten in the second-half by Marco Reus but produced a string of top-draw saves that kept Dortmund from scoring a few goals that would have rendered Balotelli's late penalty little more than a consolation.
"We didn't play well. We didn't deserve to take this point but in the end it could be important," City manager Roberto Mancini told Sky Sports.
"Borussia Dortmund played better than us and at this moment they are a better side. We need to run and fight for every ball.
"It's not enough to have just a good quality. I knew before the game it was going to be difficult as Dortmund have more experience in the Champions League than us.
"I think that Joe Hart saved us because he did very, very well. I know the problem and I will solve it very quickly. If we don't improve it will be difficult (to qualify) but this point could be important."
Dortmund's Weidenfeller was called into action after just 30 seconds to palm away a shot from Samir Nasri and superbly blocked twice from Sergio Aguero when the Argentine was through on goal.
The visitors' cause was not helped when striker Robert Lewandowski shot wide from close range and having passed up several opportunities to put the game out of sight, there was an inevitability about City's leveller when it arrived.
"We've got to b
