Clinton's remarks, too, largely lacked the self-deprecating humor that is typical at the Al Smith dinner, which benefits Catholic charities and is often one of the final opportunities for presidential candidates to share a stage before the election.
But where Clinton's remarks singed, Trump's burned -- costing him an opportunity to take some of the heat off his campaign as it struggles through the final three weeks of the 2016 contest.
"I wasn't really sure if Hillary was going to be here tonight because, I guess, you didn't send her invitation by email. Or maybe you did, and she just found out about it through the wonder of WikiLeaks," Trump said. "We've learned so much from WikiLeaks. For example, Hillary believes that it is vital to deceive the people by having one public policy and a totally different policy in private."
When the audience booed at that line, Trump said, "That's OK, I don't know who they're angry at, Hillary, you or I. For example, here she is tonight, in public, pretending not to hate Catholics."
The jeers from the audience were unusual for the event.
"I've been to that dinner like six, seven, eight times," Christine Quinn, the former speaker of New York's city council, told CNN's Anderson Cooper. "I've never heard boos like that. Never."
Also unusual for the Al Smith dinner: Neither offered any kind words about the other.
The night, which followed another brutal debate on Wednesday, underscored that Americans face a choice in two and a half weeks between two candidates who plainly don't like each other and have waged one of the most negative campaigns in recent memory.
Trump opened with light-hearted remarks -- referencing his "beautiful hands" and joking that the event with more than 1,500 attendees was for him "a small, intimate dinner with some friends. Or as Hillary calls it, her largest crowd of the season."
But the mood turned dour when Trump began to directly take on Clinton.
Trump skewered Clinton's use of a personal email server and accused her of ducking FBI questions. He pointed to WikiLeaks' hack of Democratic emails and accused her of hating the Catholics for whom the event is a high-dollar fundraiser, with attendees paying at least $3,000 each.
"According to her sworn testimony, Hillary has forgotten more things than most of us will ever, ever know -- that I can tell you," Trump said, to crickets. "We're having some fun here tonight."
Clinton takes shot at Trump's comments on women
Clinton, too, made a more direct political attack on Trump than is customary at an event that typically features light-hearted roasting.
With Trump's wife in attendance, Clinton said: "Donald looks at the Statue of Liberty and sees a 4 -- maybe a 5 if she loses the torch and tablet and changes her hair."
Clinton joked about her own personality. "I know that I am not known for my sense of humor. That's why it did take a village to write these jokes," she said.
She also lampooned the Democratic ticket -- including Virginia Sen. Tim Kaine.
"I'm not boring at all. In fact, I'm the life of every party I attend, and I've been to three," she said, adding that when parties get out of hand, they need a "chaperone to get them home safely -- and that is why I picked Tim Kaine to be my vice president."
Her remarks, too, included sharp shots at Trump. She accused him of "translating from the original Russian" when he reads off teleprompters -- a reference to Trump's coziness with Russian President Vladimir Putin.
Mocking a letter from Trump's doctor about his health that lacked specifics, Clinton said: "Donald really is as healthy as a horse -- you know, the one Vladimir Putin rides around on."
During most of the dinner, Trump sat, arms crossed, grinning during Clinton's jokes. But while Clinton looked toward the podium to watch Trump during his address, the Republican nominee mostly looked in front of him, reacting only by listening to Clinton's jokes.
When Clinton wrapped, he heartily applauded. After Clinton's remarks, Trump leaned in to say "good job."
Trump's light-hearted start
Trump started with some innocuous jokes that were well-received.
He cracked one about Melania Trump's plagiarism of a Michelle Obama speech when she spoke at the Republican National Convention in Cleveland this summer.
"Michelle Obama gives a speech and everyone loves it, it's fantastic. They think she's absolutely great. My wife Melania gives the exact same speech and people get on her case," Trump said, groaning that he'd be in trouble at home after the event.
"She didn't know about that one," he said, looking at his wife -- and then to Cardinal Timothy Dolan, sitting nearby. "Cardinal, please speak to her," he said.
Even some of his early jabs at Clinton went over well.
"We have proven that we can actually be civil to each other. In fact just before taking the dais, Hillary accidentally bumped into me -- and she very civilly said, 'pardon me,'" Trump said, a veiled reference at his debate stage pledges to appoint a special prosecutor to investigate Clinton if he wins the presidency.
"And I very politely replied, 'Let me talk to you about that after I get into office,'" Trump said. "Just kidding, just kidding."
Trump made reference to calling Clinton a "nasty woman" in Wednesday nights' presidential debate -- and compared his feelings about Clinton to his years-old beef with Rosie O'Donnell.
"After listening to Hillary rattle on and on and on, I don't think so badly of Rosie O'Donnell anymore. In fact, I'm actually starting to like Rosie a lot," he said.
The two did not shake hands or acknowledge each other on their way to their seats, though they did shake hands on the dais as the crowd mingled after the events.
During his introductory remarks, Al Smith IV said Trump asked Clinton how she was before they came on stage together. "I'm fine," Smith joked Clinton said. "Now get out of the ladies' dressing room."
Both Clinton and Trump laughed. But the GOP nominee's wife, Melania Trump, did not seem as impressed with the comment about the swirling accusations around the Republican nominee.
As Al Smith IV's locker room joke hit, Trump swayed to his side, leaning into Melania and laughing off the joke with a knowing wince.
After urging the guests to turn off their phones, Smith said, "Secretary Clinton has told me that Donald is welcome to tweet away. Apparently when Donald tweets, it makes both of them happy."
Dolan spent most of the time speaking with Clinton and almost had his back turned to Trump.
Former New York City mayor and Trump surrogate Giuliani came up behind Trump at one point, grabbed his shoulders and whispered something to him and Melania.
Minutes before he was set to address the room, Trump could be seen writing down notes on a piece of paper and then showing them to his wife. It wasn't clear if he was editing remarks or writing on a blank piece of paper.
Historically, the dinner has been a good-natured roast -- one with plenty of jokes, to be sure, but none that break with the white-tie gala's sense of decorum.
Thursday night is different, for one simple reason: Clinton and Trump loathe each other.
The two declined to shake hands at the beginning and end of Wednesday night's presidential debate, one where Trump called Clinton "such a nasty woman" and Clinton called Trump a "puppet."
Trump, in particular, has struggled to laugh at jokes told at his expense.
He famously glowered at President Barack Obama, who ribbed him at the 2011 White House Correspondents Dinner over his years of stoking false conspiracy theories about Obama's birthplace.
"He can finally get back to focusing on the issues that matter, like, did we fake the moon landing? What really happened in Roswell? And where are Biggie and Tupac?" Obama said then. Minutes later, he took a swipe at Trump's role as host of "Celebrity Apprentice."
Trump has also complained about Alec Baldwin's portrayal of him on "Saturday Night Live." After last weekend's take on Trump's performance in the second debate, he tweeted: "Watched Saturday Night Live hit job on me.Time to retire the boring and unfunny show. Alec Baldwin portrayal stinks. Media rigging election!"
A long-standing tradition
The Alfred E. Smith Memorial Foundation Dinner -- held the third Thursday of every October -- is a tradition in American presidential politics and marks the last time the two nominees share a stage.
Named for the former New York governor and first Catholic to receive a major party nomination when Democrats tapped him to oppose Herbert Hoover in 1928, the Manhattan event has an attendance of more than 1,500 donors who give more than $3,000 each to Catholic charities for tickets.