Mr Trump had been accused of racism and xenophobia for telling the members of congress to leave the country.
The president has since tweeted: "I don't have a Racist bone in my body!"
Tuesday's vote passed by 240 votes to 187 in the Democratic-controlled chamber. Four Republicans and the chamber's sole independent, former Republican lawmaker Justin Amash, joined all 235 Democrats to approve the resolution.
Texas congressman Will Hurd - the only African American Republican - was joined by his Pennsylvania member Brian Fitzpatrick, Michigan member Fred Upton and Indiana member Susan Brooks.
In a series of tweets on Sunday, the president said Representatives Alexandria Ocasio-Cortez, Ilhan Omar, Ayanna Pressley and Rashida Tlaib "originally came from countries whose governments are a complete and total catastrophe" and should "go back".
Mr Trump did not explicitly name the women - all four of whom are US citizens - in his initial Twitter tirade, but the context made a clear link to the four Democratic congresswomen, who are known as The Squad.