In its place, is a message saying it has been removed following a "report from the copyright holder".
The image included a photo of the multicoloured sweets taken by a UK-based man, who is himself a refugee.
Donald Trump Jr's post caused a furore when it was published last week, and was Twitter's highest trending item.
The graphic was based on an earlier image-less tweet by the radio talk-show host Joe Walsh.
He had alluded to the idea that some refugees posed a threat, likening this to a situation in which a person was presented with a bowl of Skittles, some of which were poisonous.
"Would you take a handful?" Trump Jr's graphic asked. "That's our Syrian refugee problem."
The photographer said he had come to the UK in 1974 as a refugee from Cyprus, and objected to the Trumps' politics.
"I am very glad it's down, and it shouldn't have been up in the first place," he told the BBC, following the image's deletion.
He added he had retained a Chicago-based lawyer over the matter, but declined to comment further.