"What's the message here, and why am I apart of it, (sic)" she wrote along with the shrug emoji.
According to People, Vogue editor Anna Wintour has similarly distanced herself from the campaign.
Both a source close to Wintour and a rep for Dunst confirmed that the use of their images was not agreed to.
The musician's on-again, off-again presidential campaign has been embroiled with controversy since the start.
Kanye launched his presidential bid at a trainwreck campaign event last month, where he broke down in tears after revealing in a monologue about abortion that he and his wife considered the option with their first child, North West.
He then flew to his ranch in Wyoming where he launched a series of extraordinary attacks on his wife Kim Kardashian and her family in tweets, sparking concerns for his mental health.
His wife later asked for "compassion" while linking his behaviour to his bipolar disorder, which the 43-year-old has spoken about publicly in the past.
Amid speculation he is running a spoiler campaign designed to siphon votes from Democrat candidate Joe Biden. earlier this month, Kanye confirmed he met with Donald Trump's son-in-law Jared Kushner, who is married to Ivanka Trump.
He said during the meeting, they discussed a book about black capitalism – Dr Claude Anderson's Powernomics.
Despite publicly backing Mr Trump in 2016 and meeting with him in the White House in 2018, Kanye more recently appeared to suggest he was no longer a supporter of the President, telling Forbes he was "taking the red hat off".
But in another interview with Forbes, he did not deny he was running a spoiler campaign, saying he was "walking to win".
Mr Trump recently told conservative radio host Hugh Hewitt that he had not talked with Kanye about the campaign, Reuters reported.
The President also told reporters he had nothing to do with the rapper's presidential bid. "I like him. He's always been very nice to me," he said.
"(He's) got a good heart, very good heart. No, I have nothing to do with him getting on the ballot. We'll have to see what happens. We'll see if he gets on the ballot. But I'm not involved."
At the moment, Kanye can only win votes in five states after missing a number of deadlines to appear on ballots.
A presidential candidate needs at least 270 electoral college votes to win the election.
