The First Minister insisted they "do not speak for me" as she addressed the daily Coronavirus briefing today.
But Ms Sturgeon stood by her position that she could not rule out quarantine for English people travelling north amid suggestions that this had contributed to the demo.
"The people that protested at the border did not speak for me," Ms Sturgeon said today.
"They were not there on my behalf and they were not there communicating a message that I endorse in any way. I don't endorse that."
A small group of Nationalists staged the demo in a layby area near the A1 at Lamberton, claiming they were seeking to keep Scotland "Covid-free".
The group was spoken to by the police.
Tory leader Jackson Carlaw has suggested that the protests may have been prompted by Ms Sturgeon's controversial warning last week that she could not rule out quarantine checks for English visitors if Covid levels diverge significantly north and south of the border.
But the First Minister said today: "This is not a question about whether people in England are welcome in Scotland. Of course they are, just as people in Scotland are hopefully welcome in England.
"It's about public health and where I have been clear is that, just as we see in other parts of the world right now, I will take decisions to protect the people of Scotland if there is a risk to public health.
"That is not political, it is not constitutional, it is certainly not based on any desire to keep English people out of Scotland."
She added: "That's not who I am and it's not what my party is about."
The First Minister referred to the situation in Australia where the border between News South Wales and Victoria has been closed after a spike in virus numbers in Melbourne.
Photographs and video footage emerged online on Saturday showing a small convoy of cars and vans festooned with Saltires, SNP flags and independence slogans parked at a rest area on the A1 route towards Berwick-upon-Tweed.
In one video, a male campaigner addresses the camera, stating: “Basically, what we’re saying is, stay the f**k out”.
But Ms Sturgeon rejected the suggestion that Scotland's reputation as an "welcoming" country will be damaged as the tourism industry emerges from lockdown.
"No I don't think it risks our reputation, because I think Scotland's reputation as an opening, welcoming international country is long standing and strong and I think it can withstand protests of that nature.
"That said I don't approve of the protests on the border because I don't think it is a particularly helpful or sensible thing to do."
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