As the man ran towards Ms Short she grimaced, picking up the dog and holding the dog close to her.
The crowd booed before breaking into applause as he was taken away.
Crufts and the NEC have said they will urgently review security measures.
In a post on its blog page, PETA wrote that the protest was organised because: "Crufts glorifies canine eugenics, rewarding breeders for producing dogs with "ideal" physical traits with little or no regard for their welfare".
"Our main priority at the moment is the wellbeing of the dogs that were in the ring, who are looked after by their owners and show officials".
It said there were two intruders and named them as members of the Vegan Strike Group, which bills itself as fighters against animal abuse.