"As you may have heard, last night the President of the United States went after me on Twitter. So Melania, if you're watching, I don't think your anti-bullying campaign is working."
Fallon also announced a donation to the Refugee and Immigrant Centre for Education and Legal Services, a non-profit immigration charity, in Trump's name.
The donation is especially relevant in light of new reports that the Supreme Court has upheld the President's ban on travel from several mostly Muslim countries today, rejecting a challenge that it discriminated against Muslims or exceeded his authority.
Trump hailed the decision, describing it as a "tremendous victory" for the American people.
"This ruling is also a moment of profound vindication following months of hysterical commentary from the media and Democratic politicians who refuse to do what it takes to secure our border and our country," he in a statement.
The feud between the President and the talk-show host started earlier this week, after Fallon told an interviewer he regretted playfully tousling Trump's hair as he didn't mean to "normalise him or to say I believe in his political beliefs".
Trump responded by blasting the talk-show host on Twitter, telling him to stop "whimpering" and "be a man".
The hair-messing TV appearance caused an outcry at the time, with critics accusing Fallon of "humanising" a person who encouraged hateful rhetoric.
In a column on the topic, Variety's then-TV critic Sonia Saraiya said the interview caused Fallon to lose "the last shred" of "any credibility as a thinking comedian with a point-of-view" that he may have had left.
Fallon has previously been criticised for not being as political as other US late-night talk show hosts, who regularly use their platforms to take on Trump.