The Anti-Defamation League said on Thursday that the triangle "is virtually identical to that used by the Nazi regime to classify political prisoners in concentration camps".
"We have removed these messages and advertisements for violating our policy against organized hatred. Our policy prohibits the use of the symbol of a prohibited hate group to identify political prisoners without the context that condemns or discusses the symbol," said Andy Stone, a Facebook spokesperson, told CNN Business.
The ads were aimed at the far left group Antifa, calling on Trump supporters to support the president's calls to designate the group as a terrorist organization.
Responding to criticism of the announcement earlier on Thursday, the Trump campaign claimed that the red triangle was "a symbol widely used by Antifa".
The paid ad was seen almost a million times in Facebook users' threads on Trump's page alone, according to Facebook data.
In a statement, Tim Murtaugh, director of communications for the Trump campaign, insisted that the red triangle is a "symbol used by Antifa.
The campaign highlighted several links to websites of t-shirts, stickers and magnets that sell merchandise with the symbol.
Murtaugh added: "We would like to note that Facebook still has an inverted triangle emoji in use, which looks exactly the same, so it is curious that they only target this ad."