Their son, Army Capt. Humayun Khan, 27, was killed by a auto bomber in 2004 in Iraq.
Trump also questioned why Ghazala, Khizr's wife, was silent during the entire speech.
In their interviews on Monday, the Khans described the outpouring of support they have received during their very public exchange with Trump. She responded in an op-ed and become emotional in follow-up television interviews. Sources reportedly would not reveal the reasoning behind the move and a statement said the campaign was "thankful to him for his many contributions and appreciate his continued support".
"I can say this if I was president - 'cause his son died 12 years ago - if I were president his son wouldn't have died because I wouldn't have been in the war".
Though Obama's comments to veterans in Atlanta on Monday afternoon didn't mention Trump by name, the President seemed to offer support to Khan's perspective.
Missouri Sen. Roy Blunt said, "My advice to Donald Trump has been and will continue to be to focus on jobs and national security and stop responding to every criticism whether it's from a grieving family or Hillary Clinton".
Mr. Trump countered by suggesting that Hillary Clinton's campaign wrote the speech. For moderate Republicans and independent voters, however, the upcoming months will be pivotal if Trump plans to woo them.
Republican lawmakers in hard re-election battles fell along the same lines, offering statements rebuking Trump with varying degrees of sternness - some attacking him by name, others simply by offering support for the Khans - but not withdrawing their support for his campaign. Trump's remarks show he doesn't understand the camaraderie between military families, he said. "They say, in presidential politics - and you guys aren't politicians, but it is just absolutely ruthless".
Sen. Charles Grassley of Iowa said Trump's comments "are not in line with my own beliefs about how the members of the military and their families should be treated".
Trump retaliated by attacking the Khizr Khan via Twitter. "McCain. This is proof of his ignorance and arrogance, and I again and again ask his advisers to get him in a room, close the door and set him right".
"In the end, I am morally bound to speak only to the things that command my allegiance, and to which I have dedicated my life's work: the Republican Party, and more importantly, the United States of America".
In a statement, McCain said Trump's disparaging of a fallen soldier's parents was against the views of the Republican party.
The Republican presidential nominee turned that statement around.
McCain thanked the Khans for coming to America, saying "your son was the best of America, and the memory of his sacrifice will make us a better nation - and he will never be forgotten".
"It's basically a manufactured controversy, manufactured by the DNC and Hilary Clinton in particular", she said, "and John McCain jumped right in". I don't think so.