The James Bond actor is taking over after The King's Speech star quit last month, admitting that he was having trouble finding the voice of the Peruvian bear.
Whishaw, 33, told the Daily Mail he was asked to audition for director Paul King's film "quite out of the blue" and was initially unsure about the project.
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"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.
Firth announced in June that he was dropping out of Paddington.
The 53-year-old Oscar winner used a term introduced by actress Gwyneth Paltrow and Coldplay singer husband Chris Martin when they recently announced their separation, to reveal that he and the movie had parted ways.
"It's been bitter-sweet to see this delightful creature take shape and come to the sad realisation that he simply doesn't have my voice," he said.
"After a period of denial, we've chosen conscious uncoupling.
"I've had the joy of seeing most of the film and it's going to be quite wonderful. I still feel rather protective of this bear and I'm pestering them all with suggestions for finding a voice worthy of him."
Director King said the split was amicable and that, although working with Firth was "a joy", they came to agree that the actor and the bear "didn't seem to fit".
The film-maker said he now feels he has found his perfect Paddington in Whishaw.
He said: "He breathes and he speaks and he sounds like Paddington, rather than the most beautiful chocolate-voiced man (Firth) on the planet."
Duffel coat-wearing, marmalade-loving Paddington was created by author Michael Bond for a series of books.
The film, due out in the UK on November 28, sees the bear despatched from his native jungle by his aunt Lucy, smuggled on board a boat to England and named after the London station where he is found.
His misadventures with his adopted family, the Browns, see him trying to evade a sinister taxidermist (Kidman).