The decision could boost Walker's re-election campaign and remove a potential obstacle as he eyes a possible 2016 presidential run.
While prosecutors quickly filed an appeal Wednesday to overturn the preliminary injunction issued Tuesday night, those who have followed this case and an earlier probe that focused on former Walker aides and associates said the ruling is a clear victory for the Republican and his allies.
"Obviously the reason this witch hunt was launched was to impugn the integrity of the governor and he has been completely vindicated," said Mark Graul, a Republican strategist who ran President George W. Bush's re-election campaign in Wisconsin.
The ruling will help to silence Walker's critics who tried to use the investigations against him, said Mike Maistelman, a Milwaukee attorney who represented Democratic and Republican elected officials in a variety of cases.
"Walker and his spin doctors around him are going to say this was a political endeavor, and that argument was backed up by the federal court," Maistelman said.
Walker, speaking to reporters following an event in Milwaukee, said he hadn't read the judge's ruling and didn't have much to say about it. He said he expected the case would continue on appeal and he'd do his best not to let it distract him.
"I don't think there's any elected official in America who's been more scrutinized than I have," Walker said. "This is just another stage in that. But we tried not to lose sight of our larger charge."
His expected Democratic opponent for re-election, former Trek Bicycle Corp. executive Mary Burke, had no immediate comment.
Walker made a national name for himself by taking on public sector union collective bargaining in 2011. The following year, he became the first governor in U.S. history to win a recall election - despite the first investigation being an issue during the campaign.
That investigation lasted three years and ended in 2013 with six convictions, including three of his former aides. Walker was interviewed but never charged.
Under Wisconsin law, prosecutors can launch John Doe investigations that are overseen by judges and conducted largely in secret. Prosecutors can compel people to produce documents and give testimony, as well as forbid them from talking about the investigation.
Walker's political opponents have been keeping a close watch on the second probe, at the heart of which was political fundraising and spending during the 2011 and 2012 recall elections. And it's taken on even greater significance as Walker considers a 2016 presidential run. Foes, including American Bridge 21st Century, a political action committee funded by liberal billionaire George Soros, have tried to paint Walker as too scandal-ridden to be trusted.
The investigation focused on alleged illegal coordination between and among Walker's recall committee and "all or nearly all right-of-center groups and individuals in Wisconsin who have engaged in issue advocacy from 2010 to the present," according to Tuesday's ruling by U.S. District Judge Rudolph Randa.
Randa issued a preliminary injunction in favor of the conservative Wisconsin Club for Growth, finding that the investigation into alleged illegal campaign coordination was an infringement on the conservative group's free speech rights.
"The plaintiffs have been shut out of the political process merely by association with conservative politicians. This cannot square with the First Amendment and what it was meant to protect," wrote Randa, who is based in Milwaukee and was appointed by President George H.W. Bush in 1992.
One of the targets of the investigation is Walker campaign adviser R.J. Johnson, who allegedly controlled a "hub" of issue-ad groups in 2011 and 2012 in coordination with Walker's campaign. Johnson did not immediately return an email or message left on his cellphone Wednesday.
The ruling left Walker allies jubilant, and if it stands, will remove a liability for Walker's re-election campaign and as he looks ahead to 2016.
Republican state Assembly Speaker Robin Vos said the ruling proved the investigation was "much more about a political agenda as opposed to fact-finding and looking for some sort of smoking gun."
Despite the ruling, Democrats won't necessarily stop trying to use the investigations to taint Walker, said Patrick Guarasci, a Democratic consultant and fundraiser.
"There is enough for both sides to make use of the investigation for their own political ends, but the everyday person is going to be very confused by the back and forth on this issue," Guarasci said. "Maybe that was the objective of the Walker side all along - to cause confusion."
Associated Press writer Dinesh Ramde contributed to this report from Milwaukee.