Attorney Bill Owens (D) held off Conservative Party nominee Doug Hoffman in Tuesday’s special election to succeed former Rep. John McHugh (R) — a topsy turvy race dominated by national political disputes in a normally quiet corner of upstate New York.

With 87 percent of precincts reporting, Owens led 49 percent to 45 percent, with state Assemblywoman Dede Scozzafava (R) drawing 5.5 percent of the vote. Hoffman conceded the race just after midnight.

Scozzafava, a moderate who was originally selected as the GOP’s nominee, dropped out of the race the weekend before Election Day and then endorsed Owens — showcasing a major ideological rift within GOP ranks. Scozzafava’s endorsement of Owens looks to have been a factor in the Democrat’s surprisingly strong performance in Jefferson County, a Republican stronghold and Scozzafava’s home base in the sprawling district.

The Democratic win in the special election prevented Republicans from a full sweep of Tuesday’s most hotly contested races, as the GOP wrested control of the New Jersey and Virginia governorships from Democrats.

The tumultuous race to replace McHugh, who resigned to become secretary of the Army, was immediately being parsed for implications far beyond the borders of the traditionally Republican but increasingly competitive 23rd district.

Owens’ victory is significant on several levels. First, it further enhances Democrats’ near-monopoly on New York’s 29 Congressional seats and leaves only two Republicans in the state’s House delegation. It also represents the second special election loss for Republicans this year in New York and signifies further erosion of the party’s ability to win seats in the northeast.

It is also highly uncommon for the party in control of the White House to flip a seat into its column. The last time that happened was in 2001, when now-Rep. Randy Forbes (R-Va.) won a special election to succeed a Democrat in the first year of the George W. Bush administration.

McHugh easily held the seat for nine terms and Republicans enjoy a 46,000-person registration advantage in the district. But voters there narrowly favored President Barack Obama last year.

Both parties and their surrogates invested heavily in the race. The Democratic Congressional Campaign Committee spent more than $1 million on independent campaign activities backing Owens. The National Republican Congressional Committee made nearly $900,000 in independent expenditures in the race, most of which were on TV ads targeted at Owens in a effort to boost Scozzafava’s campaign.

“This election represents a double-blow for National Republicans and their hopes of translating this summer’s ‘tea party’ energy into victories at the ballot box,” DCCC Chairman Chris Van Hollen (Md.) said in a statement. “Not only did eight extreme right-wing groups spend more than $1 million to drive the moderate Republican – and the NRCC’s chosen candidate – out of the race. Now, after losing a seat that was held by Republicans for nearly 120 years, they have to deal with an emboldened and well-funded far right-wing that refuses to tolerate moderate Republicans with differing opinions.”

The NRCC and House Republican leaders all initially backed Scozzafava, who was nominated in a vote by the 11 county party chairmen in the district. But Scozzafava came under attack from conservative activists over her support for abortion rights and same-sex marriage and her sympathies toward labor unions.

With the backing of a long list of Republican lawmakers and politicians, including 2008 vice presidential nominee Sarah Palin, Hoffman surged from a little known first-time candidate to the leader in final election polls released before the election, raising conservatives’ hopes of pulling off a stunning political coup.

The Club for Growth, an anti-tax national conservative group, tallied more than $1 million in advertising, mail and bundled donations as the main surrogate for Hoffman. Only after Scozzafava dropped out did the national Republican hierarchy reverse itself and endorse Hoffman.

But Ken Spain, the NRCC’s communications director, dismissed the idea of the “so-called ‘GOP Civil War,’— a recurring theme in the media coverage of the race, in a Tuesday morning memo to reporters.

And he pushed back against the notion that the intensity among the conservative base seen in the special election could present a problem for Republicans in 2010, citing examples of the same sort of rowdy left-wing battles with establishment Democrats in Washington leading up to the 2006 election.

But on Capitol Hill, even before votes were tallied, rank-and-file Republicans were divided over whether to blame party leaders for the messy New York race.

Rep. Chris Lee (R-N.Y.) expressed frustration that GOP leaders weren’t behind one candidate before sinking hundreds of thousands of dollars into Scozzafava’s campaign. While leaders backed Scozzafava, GOP Members began peeling off to support Hoffman.

“Those things need to get hammered out in advance, to get behind one candidate. That was a mistake. A lot of money was wasted that could be used for other purposes,— Lee said.

Rep. Mark Kirk (R-Ill.) launched into a more personal attack of Scozzafava, describing her campaign as “disastrous— and saying that she “personally imploded— by dropping out and then backing the candidate from the other party.

“You’ve been a Republican all your life and now you’re endorsing a Democrat? Who are you?— Kirk asked. “The failure here was the candidate. She takes all of the blame, and then some of the [local] leaders who backed her who didn’t see it.—

Kirk, who is running for Senate, said the mishap with Scozzafava illustrated “how weak— it is to have an appointed candidate in place of a primary. “Good primaries make good candidates,— Kirk said, adding the he isn’t endorsing anybody in the GOP primary for his House seat.

Some moderate Republicans said they worried that the New York race reflected a trend of conservatives becoming the voice for their party.

Rep. Mike Castle (R-Del.), who is also running for Senate next year, said he didn’t fault GOP leaders for backing Scozzafava since she was chosen by county officials and “made a very good impression— when she came to meet with Congressional Republicans. But he warned that party leaders need to focus on bringing moderates and conservatives together if they want to win back the majority.

“In the majority party, you can’t have these splits in every district between conservatives and moderates. I think it’s too bad it happened in this way— in the New York race, Castle added.