Oscar winner Firth announced he was quitting the project last month, and now producers have chosen Skyfall star Whishaw to take his place as the voice to the beloved bear.
Director Paul King tells the Daily Mail that Whishaw is the perfect replacement for Firth, saying: "He breathes and he speaks and he sounds like Paddington, rather than the most beautiful chocolate-voiced man (Firth) on the planet.
Whishaw, 33, said he was asked to audition for the film "quite out of the blue" and was initially unsure about the project.
"I resisted a little bit, because I had a bad experience doing this kind of work in the past and I thought I was no good at it. But I was persuaded to go, slightly grudgingly," he said.
The star said he is excited because his 18-month-old niece will be able to hear him in the live-action/CG blend film, which also features Nicole Kidman, Peter Capaldi, Hugh Bonneville, Sally Hawkins and Julie Walters.
But he confessed that he is mystified by the process of voicing the computer-generated bear.
"I just arrive and wear this funny helmet that has a camera attached to it. It's highly mysterious to me," he laughed.
Paddington is scheduled to hit cinemas in November.