John McCain is projected to win for the Republicans, boosting his front-runner status in his party's contest.
Mr McCain appeared to target Mr Obama in his victory speech as he promised to ensure Americans were "not deceived by an eloquent but empty call for change".
Contests are also taking place in Hawaii and Washington state.
Mr Obama is expected to win the Democratic caucus in Hawaii, where the Illinois senator was born and 20 delegates are at stake.
Polls remain open in Washington state, where Republicans are voting, until 2000 local time (0400 GMT Wednesday).
The caucuses in Hawaii do not begin until 1900 local time on Tuesday (0500 GMT Wednesday).
Seeking momentum
The BBC's Jonathan Beale says this was a significant victory for Barack Obama, marking his ninth win in a row since the votes on so-called Super Tuesday, 5 February.
It is not just about momentum, our correspondent says, but about Mr Obama eating into Mrs Clinton's support base.
Wisconsin is a largely white, working class state - the kind of place where Mrs Clinton has done well in the past, he adds.
Early exit polls suggested Mr Obama tied with Mrs Clinton for votes among women overall and substantially eroded her lead among white women, previously a core voting base for her.
He also picked up the support of six out of 10 self-described independent voters, according to exit polls for Associated Press.
With 36% of the ballots counted, Mr Obama had 56% of the vote to Mrs Clinton's 43%.
Speaking at a victory rally in Houston, Texas, Mr Obama said: "The change we seek is still months and miles away and we need to get all of Texas to help us get there."
He and Mrs Clinton have been looking ahead to March's bigger contests in Ohio and Texas, seen by analysts as crucial to her credibility as a candidate.
Some have suggested the vote in Wisconsin could be an indicator as to how she may fare in similarly industrial, blue-collar states as Ohio, and Pennsylvania in April.
Addressing a rally in Youngstown, Ohio, Mrs Clinton said the primary campaign was "about picking a president who relies not just on words but on work - hard work to get America back to work".
Before the results from Wisconsin were calculated, Mr Obama held a slight lead over Mrs Clinton, with 1,280 delegates to her 1,218.
It will take 2,025 delegates to secure the Democratic nomination at the party's national convention this summer.
McCain favourite
On the Republican side, the race between Mr McCain and Mike Huckabee, a former Arkansas governor, continues.
But Mr McCain now has almost four times as many delegates as Mr Huckabee and the support of the party establishment.
With 36% of the vote counted in Wisconsin, he led by 55% of the vote compared to 37% for Mr Huckabee and 4% for Texas Congressman Ron Paul.
Giving a victory speech in Columbus, Ohio, Mr McCain said: "Thank you, Wisconsin, for bringing us to the point where even a superstitious naval aviator can claim with providence and humility that I will be our party's nominee for president."
He went on: "I will fight every moment of every day in this campaign to make sure Americans are not deceived by an eloquent but empty call for change that promises no more than a holiday from history and a return to the false promises and failed policies of a tired philosophy that trusts in government more than people."
On Monday, former President George Bush Senior endorsed Mr McCain in his bid to be the Republicans' presidential nominee and dismissed criticism of his record as "grossly unfair".
The Washington Republican primary is the second half of a two-part nominating contest. The state's Republicans held a caucus on 9 February, which was narrowly won by Mr McCain.
Republicans will only allocate about half their delegates on the basis of the primary - the rest were decided earlier in the caucus.
Washington state's Democrats are also holding a primary but their delegates to the party's summer nominating convention have already been chosen on the basis of caucuses.
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