The Afghan-born 28-year-old was charged with five counts of attempted murder after a police shootout.
The Republican nominee said it was a “sad situation” and underscores the country’s weak national security.
Meanwhile, his Democratic rival Hillary Clinton said Mr Trump’s rhetoric only helped terrorist groups.
“The kinds of rhetoric and language that Mr Trump has used is giving aid and comfort to our adversaries,” Mrs Clinton told reporters at a news conference outside New York City.
She added that she was the only candidate equipped with the experience of being “part of the hard decisions to take terrorists off the battlefield”.
Mr Trump fired back in a statement, saying that a Clinton presidency would only lead to “more attacks on our homeland and more innocent Americans being hurt and killed”.
Later at a campaign rally in Fort Myers, Florida, Mr Trump decried Mr Rahami’s treatment for gunshot wounds and his legal representation, which is his constitutional right under the Fifth Amendment.
“But the bad part, now we will give him amazing hospitalization. He will be taken care of by some of the best doctors in the world,” Mr Trump said.
“He will be given a fully modern and updated hospital room. And he’ll probably even have room service knowing the way our country is.”
He suggested that any punishment would be too lenient on Mr Rahami. “What a sad situation,” he added.
Mr Trump repeated calls for “extreme vetting” of new arrivals, which would include an assessment of whether potential immigrants share American values.