Wallace responded with an uplifting message "to the next generation" - and a denunciation of the president.
The 26-year-old encouraged his fans to embrace "love over hate every day... even when it's hate from the POTUS," referring to the president.
Trump's tweet was his latest divisive rhetoric - he also spoke out on Monday about US sports franchises considering changing their Native American-themed team names - ahead of November's presidential election.
The noose discovery was made shortly after Wallace had successfully campaigned for a ban on flying the controversial Confederate flag at NASCAR, a popular sport with conservative Americans.
Trump also claimed in his tweet that the ban and the noose controversy had "caused lowest ratings EVER!"
The President's remarks came after two divisive Independence Day weekend speeches which critics said were an attempt to exploit racial animus and stoke fear among his base of white supporters, four months ahead of the presidential election.
Last week Trump, who is trailing presumptive Democratic challenger Joe Biden in the polls, shared a video of his supporters chanting "white power" - before deleting it amid an outcry.
NASCAR president Steve Phelps noted after the inquiry had finished that "the noose was real" and "our initial reaction was to protect our driver."
"In hindsight, I should have used the word 'alleged' in our statement," said Phelps.
The United States has been upended by coast-to-coast protests since the May killing of African American George Floyd by police in Minneapolis.
The demonstrations have seen attacks on symbols of the country's slave-holding history such as the Confederate flag and statues of Confederate generals.
Trump has branded the movement a "left-wing cultural revolution" and an assault on American "heritage," and vowed to resist it.
The White House slammed the media over the Wallace clash, saying reporters were "mischaracterising" Trump's words.
"The intent of the tweet was to stand up for the men and women of NASCAR and the fans, and those who have gone in this rush to judgment of the media to call something a hate crime, when in fact the FBI report concluded this was not an intentional racist act," Press Secretary Kayleigh McEnany said.
McEnany also declined to say whether Trump agrees with NASCAR's decision to ban the rebel-themed flag, saying the president has not made a judgment "one way or the other."
Trump also weighed in on two sports teams that are considering changing their names and logos amid renewed calls for social justice and civil rights.
"They name teams out of STRENGTH, not weakness," Trump said in a tweet that mocked efforts to avoid marginalising certain minority groups.
"But now the Washington Redskins & Cleveland Indians, two fabled sports franchises, look like they are going to be changing their names in order to be politically correct."