Bobi died in October at the official age of 31 years and 165 days.
But now his title has been thrown into doubt, after some veterinarians questioned evidence of Bobi's age.
GWR have now suspended the title and launched an investigation.
Bobi was a purebred Rafeiro do Alentejo - a breed that has an average life expectancy of 12 to 14 years.
His grand old age was validated by the Portuguese government's pet database, which is managed by the National Union of Veterinarians, GWR said last year.
But as news of his crowning rapidly spread - so too did suspicion.
An investigation by Wired magazine found that Bobi had been registered on Portugal's pet database as having been born in 1992, but it had "no registration or data that can confirm or deny this statement".
There were also questions over old photos of the pet that showed different markings on his fur, with some suggesting it was a different dog altogether.
Some experts have said they doubt Bobi was actually 31
Among experts, there has been growing scepticism.
Danny Chambers, a member of the Royal College of Veterinary Surgeons, told The Guardian: "Not a single one of my veterinary colleagues believe Bobi was actually 31 years old."
Now, Guinness World Records have launched a formal investigation.
"While our review is ongoing, we have decided to temporarily pause applications on both the record titles for oldest dog living and (oldest dog) ever until all of our findings are in place and have been communicated," a spokesperson told the AFP news agency.
Bobi lived his whole life with the Costa family in the village of Conqueiros, near Portugal's west coast.
His owner, Leonel Costa, said in a statement that "an elite within the veterinary world... tried to give people the idea that Bobi's life story was not true".
Mr Costa believes the backlash came because he attributed Bobi's longevity to eating a diet similar to that of humans, rather than pet food. He says this goes against the recommendations of many veterinarians.
"Everything would be different if we had said he ate pet food for three decades," Mr Costa said, adding that everything GWR had requested to validate Bobi's age had been met.
Until Bobi's death, the previous oldest dog ever was Australia's Bluey, who died in 1939 at the age of 29.
By George Wright