Young Trump's tweet said, "This image says it all. Let's end the politically correct agenda that doesn't put America first."
His father has advocated sharply restraining immigration and has accused opponent Hillary Clinton of advocating acceptance of tens of thousands of refugees.
Skittles parent company Wrigley Americas distanced itself from the tweet with a terse response opposing Trump Jr.'s premise.
"Skittles are candy. Refugees are people. We don't feel it's an appropriate analogy," Vice President of Corporate Affairs Denise Young said in the statement. "We will respectfully refrain from further commentary as anything we say could be misinterpreted as marketing."
The tweet came as world leaders meeting at the United Nations on Monday approved a declaration aimed at providing a more coordinated and humane response to the global refugee crisis, among which Syrians are a major grouping.
During the campaign Trump has repeatedly called for a moratorium on accepting Syrian refugees. This is part of a more wide-ranging policy on immigrants that has ranged from an outright ban on foreign Muslim immigrants entering the United States "until we know what the hell is going on" to "extreme" vetting and an ideological test for would-be immigrants from countries and regions plagued by extremism.
Clinton has said she would expand President Barack Obama's refugee program to accept about 65,000 Syrian refugees. This would be in addition to the tens of thousands of refugees accepted from around the world every year. Clinton said she would continue with the vetting currently in place, an effort that can take multiple years to complete.
Hundreds of thousands of Syrians have sought refuge in Europe while many others wait in neighboring countries and refugee camps for the war to end or a chance to move away from the carnage. Obama pledged the U.S. would accept 10,000 Syrians this budget year, which ends Sept. 30, and achieved that number a month early. This is in addition to about 75,000 refugees from other parts of the world.