With nearly three-quarters of precincts counted, Chaffetz led Cannon by more than 20 points. Chaffetz now advances to face Democrat Bennion Spencer in November. The seat strongly favors Republicans.
Cannon, meeting with backers gathered at the Historic Utah County Courthouse in Provo, was not conceding defeat, but said a loss would not be the end of the world.
"Either we win or we lose, but politics doesn't end," said Cannon, sunburned from a day of doing honk-and-waves.
In many ways, the battle between Chaffetz and Cannon is a snapshot of national trends, reflecting a discontent with Congress, high gas prices and a shaky economy.
Chaffetz, 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 eliminating the federal government's role in public education.
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.
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 Bennet, and spent tens of thousands of dollars on polling.
Chaffetz and his fleet of volunteer staff put their efforts into organizing a grassroots effort.
A poll conducted last week by Brigham Young University found widespread discontent with the current state of the country in the 3rd Congressional District, indicating voters were looking for a change.
"It's not the best time to be part of the Washington establishment, incumbent member of Congress crowd, so you may find that people will go more heavily for Chaffetz, not because they know much about him, but because they're against Cannon," said Quin Monson, assistant director of BYU's Center for the Study of Elections and Democracy. "It's a tough environment for Cannon to be in."
The Cannon campaign spent weeks trying to identify the congressman's supporters and will be pulling out the stops to make sure they get to their polling places on Tuesday. Chaffetz has 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 legal 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.