Baker, who won an army of fans for his athletic performances as runner-up in last year's Strictly Come Dancing, had long been the frontrunner to land the job.
He replaces Jason Manford who quit the magazine show after it emerged the married presenter had been exchanging lewd messages with female fans by text and Twitter.
Baker, who first found fame as a Blue Peter presenter, had been a success as a stand-in on The One Show. But he has been busy with rehearsals and performances for the Strictly tour for the past few weeks. He will continue to present Countryfile.
Baker, who will take his place alongside co-host Alex Jones from February 14, said: "I'm over the moon to be joining The One Show as a full-time presenter.
"The BBC has made everything possible so I can also continue presenting Countryfile. It's the ideal combination for me and I can't wait to get started."
The popular BBC1 show had to renew its presenter line-up after Adrian Chiles and Christine Bleakley headed to ITV last year, with Jones and the short-lived Manford taking over.
Baker landed two TV Baftas during his seven-and-a-half year stint on Blue Peter.
Jones said she was pleased Baker was to become a "permanent fixture".