Bayer fell behind after 14 minutes when veteran Romanian international Gheorge Popescu struck for Hanover.
But ten minutes from time Marko Babic crossed for Sebastian Schoof to equalise and two minutes into added time Oliver Neuville played in Jan Simak to clinch all three points.
After the game caretaker manager Thomas Horster admitted: "There is no doubt we were lucky.
"But our heads are free now, and we can build from this.
"We're back again."
Meanwhile Leverkusen midfielder Yildiray Basturk has been stirring up controversy ahead of Wednesday’s Champions League game by claiming that Alan Shearer should move to the Bundesliga.
"Where were the English teams when the Champions League final was being played last time," said the Turk.
"Bayer were in it – not Newcastle, Arsenal or Man United. And that’s a fact.
"People have asked me about a move to England, but why should I do that?
"Players like Juan Sebastian Veron, Alan Shearer and Thierry Henry should come to Germany."
He may have a fair point about last season, but does anyone think that Bayer or any of the other German teams will reach the final this season?