A number of fans and critics have expressed difficulty understanding the villain's dialogue in the six-minute prologue to the highly-anticipated film.
The screenwriter, who is brother to director Christopher Nolan, spoke about Hardy's depiction of Bane while attending a panel for his show Person of Interest at the TCA press tour.
"I've gotta tell you, I think what Tom Hardy is doing with the role is spectacular," Jonathan said. "I've had the benefit of seeing a little bit more than the audience has seen, at this point, and it's pretty spectacular."
Jonathan went on to speak about the airborne action sequence that takes place in the prologue.
"It's an amazing team with my brother, [story writer] David [S] Goyer and myself," he said. "Those are two great guys to work with and brainstorm with.
"I think Chris [has] long wanted to do the aerial spectacular. It's such a good fit for the IMAX cameras that he likes to shoot with, and so that was a long time in the making."
It was recently alleged that a new audio mix for the Dark Knight Rises prologue had been sent to cinemas in order to clean up Bane's dialogue, although Warner Bros later denied the report.
The Dark Knight Rises opens in cinemas on July 20, 2012.
Watch the trailer for The Dark Knight Rises below: