Speaking at a campaign rally in Toledo, Ohio, the Democratic presidential nominee attacked her Republican opponent as representing "the same rigged system that he claims he's going to change."
"While millions of American families, including mine and yours, were working hard and paying our fair share, it seems he was contributing nothing to our nation. Imagine that," Clinton said. "In other words, Trump was taking from America with both hands and leaving the rest of us with the bill."
The Times story, Clinton said, "tells us everything we need to know about how Trump does business."
"After he made all those bad bets and lost all that money, he didn't lift a finger to protect his employees, or all the small businesses or the contractors he'd hired, or the people of Atlantic City," she said. "They all got hammered while he was busy with his accountants trying to figure out how he could keep living like a billionaire."
Clinton also mocked Trump for his massive losses during the 1990s, saying they undercut Trump's claim that he is a successful businessman who can help revive the US economy.
"Here is my question: What kind of genius loses a billion dollars in a single year?" Clinton said.
The New York Times story, which published online Saturday evening, has the potential to be deeply damaging for Trump in the final weeks of the presidential election.
Through an examination of portions of Trump's 1995 tax records, the New York Times determined that Trump declared $916 million in losses in his 1995 income tax returns -- "a deduction that could have allowed him to legally avoid paying any federal income taxes for up to 18 years," the article stated.
The Times did not look at Trump's federal return. It obtained one page of his New York State resident income tax returns as well as the first page of New Jersey and Connecticut nonresident returns. CNN has not independently verified the documents, but the Trump campaign has not questioned their accuracy.
The story offers powerful ammunition to Clinton as the 2016 campaign enters its final homestretch.
The former secretary of state has already been highly critical of Trump and his tax returns during the general election. She has gone after the real estate investor for defying the tradition that modern presidential nominees have followed by refusing to release his tax returns (Trump insists it is because his recent returns are under IRS audit, though that does not preclude him from making them public).
During the first debate last week, Clinton suggested that Trump was hiding something -- including, potentially, that "he's paid nothing in federal taxes."
In Ohio on Monday, Clinton once again suggested that Trump must be covering up something.
"You may have heard that he has long refused to release his tax returns the way every other nominee for president has done for decades," she said. "What is he hiding? It must be really terrible."
Clinton's top surrogates are also getting in the action.
Vice President Joe Biden, campaigning for Clinton in Orlando and Florida on Monday, said: "(He) says, 'I didn't pay any federal taxes possibly for more than 18 years.' He said, 'that makes me smart.' What does that make the rest of Americans?"
Trump went on offense Monday in his first rally since The New York Times story published. Speaking in Pueblo, Colorado, Trump said he has "brilliantly used" tax laws to his benefit and downplayed his alleged financial losses from the 1990s.
"The news media is now obsessed with an alleged tax violation from the 1990s, at the end of one of the most brutal economic downturns in our country's history," Trump said
Monday marked the first time Clinton has campaigned in Ohio since Labor Day. Recent polls have shown Trump with a small advantage in his heavily white and working-class state.
But the Clinton campaign and its allies insist that the state is still within reach, and that Ohio is a must-win for the Republican nominee. As a part of the strategy to appeal to blue-collars workers in this region, Clinton on Monday went after what she called "egregious corporate behavior" that undermines the middle-class.
One of her prime targets was Wells Fargo and the recent revelation that the bank created a slew of accounts without customers' consent to collect fees.
"Look at Wells Fargo -- really shocking, isn't it?" Clinton said. "One of the nation's biggest banks, bullying thousands of employees into committing fraud against unsuspecting customers, secretly opening up millions of accounts for people without their consent, even their knowledge, misusing their personal information and sticking customers with hidden fees."