The chant was directed at Somali-born lawmaker Ilhan Omar, though Mr Trump had also attacked three other non-white lawmakers during his speech.
Ms Omar, who is a US citizen, responded on Twitter by quoting a poem by civil rights activist Maya Angelou.
Ahead of the rally, a bid to impeach Mr Trump was blocked in Congress.
The controversial chants took place at Mr Trump’s campaign rally in North Carolina.
Mr Trump was cheered on by the crowd of thousands as he again accused Ms Omar and her fellow congresswomen Alexandria Ocasio-Cortez, Rashia Tlaib, Ayanna Pressley – known as “the squad” – of hating America.
Critics say it echoed the “lock her up” phrase adopted by his supporters against Hillary Clinton in the run-up to the 2016 presidential election.
What’s the reaction?
In response, Ms Omar tweeted lines from Maya Angelou’s poem Still I Rise: “You may shoot me with your words…But still, like air, I’ll rise.”
She later shared a photo of herself in the House of Representatives, saying, “I am where I belong”.
On Twitter, #IStandWithIlhan began trending as Democrats expressed their support for Ms Omar and criticised the president for prompting the chants with his rhetoric.
Democratic presidential hopeful Senator Bernie Sanders tweeted: “Trump is stoking the most despicable and disturbing currents in our society.”
Senator Kamala Harris, another Democratic 2020 contender, described the actions as “vile”.
Senate Democratic leader Chuck Schumer drew comparisons to dictatorships.
Speaker of the House Nancy Pelosi simply told reporters: “We condemned the president’s comments the other day. That’s our statement.”
Some conservatives have also censured the use of the phrase.
Chairman of the National Republican Congressional Committee Tom Emmer – who, like Ms Omar, represents Minnesota in Congress – told reporters he did not agree with the language.
“There’s no place for that kind of talk,” Mr Emmer said, according to Politico, though he stopped short of calling the chants racist. He said the chant was “not acceptable”.
North Carolina congressman Mark Walker said that he “struggled” with the chant and that the focus should be on “her history, words & actions” instead of “phrasing that’s painful to our friends in the minority communities”.
His fellow Republican Adam Kinzinger said the chants were “ugly”.
Conservative commentator Ben Shapiro said “chanting for her deportation based on her exercise of the First Amendment is disgusting”.
Senator Lindsay Graham, a vocal Trump supporter, defended the president, though he said he wished Mr Trump would focus on “policies not the personality”.
“I’ve said before that if you’re a Somali refugee wearing a Maga hat, he doesn’t want to send you back. You’d probably have dinner at the White House,” Mr Graham told reporters.
The South Carolina Republican added: “I don’t like it – I’m not going around telling anybody to leave the country who’s an American citizen.”
Republican leader Mitch McConnell told the Fox Business Network on Thursday that Mr Trump is “on to something” by attacking the four congresswomen as their policies will be important in the upcoming election.
“We’re in a big debate now and next year about what we want America to be like. Do we really think socialism applies here at a time of great prosperity, 50-year-low unemployment?”
A recipe for a toxic campaign
Three years ago, crowds at Donald Trump rallies called for the imprisonment of a political adversary. On Wednesday, they chanted for a member of the opposition party to be expelled from the country.
These are not behaviours emblematic of a healthy, well-functioning democracy.
The president’s defenders have parsed his incendiary language in an effort to explain why telling people to “go back” to the “totally broken and crime infested places from which they came” is not simply the latest iteration of age-old racist invective. It was, they insist, just a Trumpian twist on “love it or leave it” sloganeering.
When the rhetoric filters down to the president’s vocal crowds, however, such nuance is lost.
Mr Trump is an instinctual politician who senses weakness and opportunity and often acts before a strategy is fully formed. The goal, however, is clear. He is both trying to sow divisions within Democratic ranks and rile up a base whose enthusiastic turnout will be needed in the coming election.
Such a course is not without risk, however. His actions could motivate and unify opponents as much as they do his base. It’s a recipe for a toxic, divisive campaign that will get ugly – and fast.
What else has Mr Trump said?
In an interview with the Daily Mail just before the Greenville rally, Mr Trump said he was “not unhappy” with the way the row has played out and said he believes he is “winning the political fight…by a lot”.
“I’m not relishing the fight,” Mr Trump said. “I’m enjoying it because I have to get the word out to the American people. And you have to enjoy what you do. I enjoy what I do.”
He added: “I think that they are not espousing the views of our country, the four congresswomen.”
“The only thing they have, that they can do is, now, play the race card. Which they’ve always done.”
What’s the background?
The chanting stems from Mr Trump’s attacks on the women from this weekend, where in a series of tweets, he told the then unnamed politicians to “go back” to their countries.
The president has denied accusations that the tweets were racist, but the Democrat-controlled House passed a symbolic resolution denouncing Mr Trump’s “racist comments that have legitimised fear and hatred of New Americans and people of colour”.
A July poll by the Pew Research Center found that while 62% of overall Americans believe openness to people from around the world is “essential to who we are as a nation”, 57% of Republicans said the US risks “losing our identity as a nation” if it is too open.
Earlier on Wednesday, a bid to launch impeachment proceedings against Mr Trump was blocked in the US House of Representatives after it failed to win enough support, with only 95 Democrats voting in favour.
Mr Trump said the “ridiculous” attempts to impeach him were now “over”.