The 23-year-old Belgian rider for Quickstep hoisted his arms in the air at the finish after dashing ahead of Australian Stuart O'Grady of Cofidis, who finished second, and Germany's Erik Zabel of T-Mobile, who placed third.
"It was really a great win," said Boonen, a former U.S. Postal Service teammate of Armstrong, riding in his first Tour. "I love this kind of sprint — hard — for really strong sprinters."
Armstrong and his chief rival — Germany's Jan Ullrich of T-Mobile — managed to stay clear of a major wreck near the finish line that involved all but about 30 riders.
According to sporting rules, competitors who are held up in a crash in the final kilometer of a stage must be given the same time as the winner. Thus, Boonen and a massive pack of riders, including Armstrong and Ullrich, clocked 4 hours, 33 minutes and 41 seconds in the stage. Ullrich was 26th and Armstrong, 34th.
The fast-paced sixth stage took place without two of cycling's fastest sprinters — Italians Mario Cipollini and Alessandro Petacchi, who pulled out of the race before the start due to injury.
That created an opportunity for sprinters like Aussie Robbie McEwen of Lotto Domo. But McEwen was one of those caught in the crash, and he rode slowly to the finish line with a huge hole in his racing shorts after painfully sliding along the tarmac.
Frenchman Thomas Voeckler retained the overall leader's yellow jersey. Armstrong remains 9 minutes, 35 seconds back in sixth place, and Ullrich trails him by 55 seconds.
Armstrong fell about 20 minutes into the 122-mile stage from Bonneval to Angers, but recovered to catch up with help from his U.S. Postal Service team. He was unhurt except for a couple of minor scrapes.
"It was a typical early race crash," he said. "There's nothing you can do. You hit the brakes, but bikes don't stop that fast, so I just went over."
Armstrong said he was not seriously hurt.
"It wasn't bad, a little bit on the arm, a little bit on the hip," he said.
The five-time champion also criticized organizers for the narrow layout of the final stretch into the finish.
"Coming in, they've got the barriers really tight, and you've got 200 guys racing through there at 40 miles an hour. I don't know what the hell they're thinking, but you're going to have crashes," Armstrong said.
The spill was the 32-year-old Texan's first in a crash-marred first week for riders often battling wind, rain and chilly weather. But his bid for a record sixth Tour crown was not derailed.
Armstrong had said a day earlier that he was worried about crashing. Adverse conditions marred much of the first week, though Friday's stage was balmy by comparison and mostly rain-free.
"In this race, I'm always scared, always nervous," he told reporters. "The last two or three days for me, personally, have been really, really nerve-racking."
"It's a stressful race," he added.
Viatceslav Ekimov of Russia, Armstrong's trusted sidekick who usually steers him through crashes and other hazards, arrived last and battered at the Postal Service bus with a thin stream of blood running down from his right knee. Five Postal riders were among the top ten in the overall standings at the stage end.
Fellow American Tyler Hamilton, a Phonak rider considered to be a threat to Armstrong's bid, blew a tire but also caught up with the main group near the 36-mile mark. Hamilton was 102nd in the stage and 13th overall.
By Jamey Keaten