With 99 percent of the votes counted, Chaffetz led Cannon by about 20 points. Chaffetz now advances to face Democrat Bennion Spencer in November. The seat strongly favors Republicans.
With Chaffetz holding an insurmountable lead late Tuesday, Cannon refused to concede until nearly 11 p.m. He said that, while he is leaving Congress, he is not leaving politics, and committed to work to getting Republicans around the country elected, including Chaffetz.
"We had a small race and the people of Utah have spoken," said Cannon, who believed low turnout was a factor in the election, but the war in Iraq and President Bush's sagging popularity were not.
"Bush has the highest rating in Utah, and that says the people support him and the war," Cannon said. "Their frustration is directed elsewhere."
The battle between Chaffetz and Cannon saw many of the larger political trends - discontent with Congress, high gas prices and a shaky economy - play out on a small scale.
"It's just such a tough environment for incumbents," said Kelly Patterson, director of the Center for the Study of Elections and Democracy at Brigham Young University. "President Bush had low approval ratings, Congress had low approval ratings. People are dissatisfied with the way Congress and Washington work and Representative Cannon was seen as a part of that."
Chaffetz, 41, who is president of the consulting firm Maxtera Inc., and former chief of staff to Gov. Jon Huntsman Jr., launched his campaign nearly two years ago, meeting with Republican delegates to lay the groundwork for his challenge.
Chaffetz hammered away at Cannon, running a relentless campaign targeting Congress' failure to control government spending, fix immigration and energy policies, and vowing to eliminate the federal government's role in public education.
"The Republican Party is broken and I want to fix it," said Chaffetz, as his supporters celebrated, drinking apple beer at a gathering in Springville.
Cannon has cited his conservative credentials, his work to develop oil shale in order to bring down gas prices, and said he has the experience and seniority to represent the district in Washington.
In the primary's last days, he also criticized Chaffetz for not living in the 3rd District. While that is legal, it is unusual. In fact, Chaffetz is the only one to pull it off in recent memory.
It was the third straight election in which Cannon was forced into a primary. But in the previous two contests, his opponents proved less skilled politicians than Chaffetz and based their campaigns almost exclusively on opposition to illegal immigration.
Chaffetz fell 10 votes shy of eliminating Cannon at the Utah Republican Convention, forcing him to a primary. Cannon out-raised Chaffetz by nearly 7-to-1, had the endorsements of President Bush and Sens. Orrin Hatch and Bob Bennett, and spent tens of thousands of dollars on polling.
Chaffetz and his fleet of volunteer staff put their energy into organizing a grass-roots push.
"This was an anti-government vote," said John Updike, a Cannon supporter from Provo, who also blamed low turnout and complacency for Cannon's poor showing.
A poll conducted last week by Brigham Young University found that about 80 percent of voters in the 3rd Congressional District thought the country was on the wrong track, indicating a clear appetite for change.
"[Chaffetz] clearly was able to ride a wave, but there was a wave there to ride," said Patterson.
The Cannon campaign spent weeks trying to identify the congressman's supporters and pulled out the stops to make sure they got to their polling places on Tuesday. Chaffetz had identified captains in each precinct in the district responsible for getting his voters to the polls.
Holly Richardson, who has 20 adopted children, said she felt like Chaffetz "walked the walk with his fiscal discipline," and liked his stance on fixing illegal immigration and repealing the No Child Left Behind Act.
"This is the first campaign I've helped on. None before Jason's have grabbed me," she said.
* SHEENA MCFARLAND and DONALD W. MEYERS contributed to this report.