"The President's words weigh a tonne, and his hateful and inflammatory rhetoric creates real danger", she said in a statement while travelling in London.
The video was no longer a pinned tweet at the top of Mr Trump's Twitter feed, but it had not been deleted.
"She is out of control, except for her control of Nancy!" he said of Ms Omar.
"For too long we have lived with the danger of being a second-class citizen, and frankly, I'm exhausted of it".
Omar was speaking at a CAIR banquet in California in March when she made her controversial remarks about 9/11.
"For far too long we have lived with the discomfort of being a second-class citizen and, frankly, I'm exhausted of it, and every single Muslim in this country should be exhausted of it", Omar's full quote said.
Omar in her statement Sunday night said Trump was encouraging violence - which Sarah Sanders denied earlier Sunday in an appearance on ABC's "This Week".
Celebrities, activists and politicians, including many who have criticised Omar in the past for comments on Israel, came to Omar's defence under #IStandWithIlhanOmar. She tweeted back at Kilmeade and Crenshaw: "This is unsafe incitement, given the death threats I face". In doing so, and by refusing to pledge allegiance to Israel, she's faced vicious smears calling her antisemitic (including from Trump).
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Omar said in a statement posted on Twitter Sunday that numerous increased threats she had received were "directly referencing or replying to the President's video".
Ilhan Omar (D-Minn.), accusing the legislator of "U.S. HATE" and saying she has "control" over House Speaker Nancy Pelosi. Almost one in three Somali-Americans live in the state, according to the U.S. Census Bureau, and between 42,400 and 55,200 people - about 1 percent of the population of the state - is of Somali heritage, according to recent census data.
Trump's tweet (still up at the time of writing) intercut images of Omar with video footage of 9/11.
"I'm not going to tell the president what he should or should not do with the Twitter account", Lotter said. Instead, she blamed Democrats for refusing "to call" Omar for what she termed anti-Semitic comments.
Their latest spat concerns Omar's remarks about the treatment of American Muslims since the September 2001 terror attacks on NY and Washington.
Sanders, who would be the first Jewish president if elected in 2020, has argued repeatedly that the American government must take a harder line against Prime Minister Benjamin Netanyahu's government over its treatment of Palestinians.
Independent Senator Bernie Sanders who is also a Democratic presidential candidate, wrote on Twitter: "Ilhan Omar is a leader with strength and courage".