Tease the Whippet scooped the coveted crown after a flawless display on the famous green carpet at the world's biggest dog show - held once again at the NEC Arena - on Sunday evening.
The intruder was carrying a banner bearing the logo of PETA (People for the Ethical Treatment of Animals).
Applause broke out as the intruders were removed from the arena floor.
By storming the stage, they left a number of dogs scared, putting the safety of the animals and their owners at risk.
Crufts and the NEC have said they will urgently review security measures.
The post then goes on to list specific breeds which, it says, have been negatively impacted by "extreme breeding", including: "The "pushed-in" faces of English bulldogs and pugs make it so hard for them to breathe that many can't even enjoy the activities that dogs love, such as chasing a ball or going for walks, without struggling for air".
An intruder is wrestled to the ground after Tease the Whippet was named Supreme Champion during the final day of Crufts
Campaigners for animal rights, said to be from Peta, entered the Crufts arena as the top prize was about to be awarded in protest against "extreme breeding".
A protestor is carried off after running into the area as Best In Show was being announced on day four of Cruft's. "She took it more in her stride than me but we did it!"
Host Clare Balding told her: "Well done you for reacting so quickly, your instinct was to protect Tease".
"We are not sure what we are going to do with the dog yet as she's only two-and-a-half, so we'll see when we get home".
Milly added: "Shaking for ages after the #Crufts invader".
Sally Simpson echoed the sentiments: "Absolute credit to the woman in Crufts who protected her dog before she even thought of herself with the stage intruder".