June 24, 2014 11:21 PM EDT

Sen. Thad Cochran narrowly won Mississippi’s Republican primary election Tuesday, prevailing over a Tea Party challenger in a hard-fought runoff vote that was seen as a proxy for the intramural fight between the GOP establishment and conservative insurgents.

Cochran, a six-term incumbent, beat two-term state Sen. Chris McDaniel, a former talk-radio host with strong Tea Party support, by just a few thousand votes. The Associated Press called the race for Cochran a few minutes after 11 p.m. E.T. With 98.1% of precincts reporting, Cochran had 50.7% of the vote to McDaniel’s 49.3%. McDaniel had bested Cochran by a half-a-percentage point in the initial June 3 primary, but neither man won a clear majority, forcing the two into a runoff that culminated Tuesday. Cochran strategists called the June 3 primary a wake-up call for a candidate who had run a scattershot campaign up to that point.

“We all have a right to be proud of our state tonight,” Cochran told supporters Tuesday night.

“What we have tonight is reflected as a consensus for more and better jobs for Mississippi workers, a military force and the capacity to defend the security interests of the United States of America,” Cochran said. “Those were our principle… planks in the platform of the campaign.”

Cochran’s campaign had looked to expand the electorate after falling short in the runoff, heavily courting black voters and other traditionally Democratic constituencies (Democrats were allowed to vote in the runoff Tuesday if they hadn’t voted in the June 3 Democratic primary). That strategy — Cochran strategists called Democratic turnout a key factor in the narrow race — drew outrage from McDaniel supporters and promises to monitor polling places for any shenanigans. McDaniel did not concede Tuesday night and quickly tried to cast doubt on the outcome. He claimed there were “dozens of irregularities” in voting across the state and went so far as to suggest that he may bring a legal challenge. Mississippi state law does not include a recount provision, leaving McDaniel with the courts as his only — however unlikely — recourse.

“There is something a bit strange, there is something a bit unusual about a Republican primary that’s decided by liberal Democrats,” McDaniel told supporters. “Before this race ends, we have to be absolutely certain that the Republican primary was won by Republican voters.

“So much for bold colors. So much for principle,” he added. “I guess [we] can take some consolation in the fact that they did something tonight. By once again compromising. By once again reaching across the aisle. By once again abandoning the conservative movement. … Today the conservative movement took the backseat to liberal Democrats in the state of Mississippi.”

The nominating contest drew national attention as it developed along clear ideological lines between conservative Tea Party activists supporting McDaniel and GOP establishment figures backing Cochran, mirroring the wider civil war boiling in the party. An incumbent with decades of experience in Washington, Cochran earned a reputation in his career for bringing federal dollars into Mississippi, something for which McDaniel supporters labeled him the “King of Pork.”

The election drew millions of dollars in outside spending from national entities like the conservative Club for Growth and Sarah Palin for McDaniel, and the Chamber of Commerce and John McCain for Cochran. The race also took some nasty turns, as voters were inundated with accusations and counter-accusations that flew back and forth in negative ads. At one point, a group of McDaniel supporters were caught taking pictures of Cochran’s ailing wife in a nursing home.

Cochran will go on to face Democrat Travis Childers in November’s general election. Though weakened after a drawn out, internecine battle, Cochran, who has more than 40 years under his belt as a Mississippi politician, is likely to emerge victorious in the deeply conservative state.

— Additional reporting by Zeke J Miller

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