Mrs Clinton wanted the committee, meeting in the ballroom of a Washington hotel, to overturn a previous decision and allow delegates from Florida and Michigan to vote at the Democratic National Convention in August.
Delegates to that convention, chosen in votes in each state, will decide which politician becomes the Democratic Party candidate in November's presidential election.
Officially, Mrs Clinton won both states, but both were initially discounted because they held their primaries in January, in contravention of party rules.
Neither candidate campaigned in the contests, and in Michigan, Mr Obama's name was not even on the ballot.
Hillary Clinton was campaigning in Puerto Rico on Saturday
The compromise gives Mrs Clinton 69 delegates in Michigan, compared to Mr Obama's 59. And in Florida, she gains 105 delegates to Mr Obama's 67.
This reduces Mr Obama's lead - previously 202 - by 48, but the delegates from Michigan and Florida will only have half a vote each, so her gains are reduced.
The 27-member committee unanimously accepted the compromise decision for Florida, after earlier rejecting by 15-12 a plan which would give all delegates full voting rights at the convention.
In the case of Michigan, the committee approved the compromise by 19-8.
Overall, Mrs Clinton gains only 24 delegate votes, far short of the total she needs to catch Mr Obama.
Mrs Clinton is still hoping to persuade undecided "super-delegates" that she should be the party's nominee.
Mr Obama speaks about the delegate decision on Florida and Michigan
Her adviser Mr Ickes accused the committee of "hijacking" votes for Mrs Clinton.
"Mrs Clinton has instructed me to reserve her rights to take this to the credentials committee," he added.
The Obama campaign greeted Saturday's votes as a "fair solution that will allow Michigan and Florida to participate" in the party convention in Denver in August.
During the day's voting, Clinton supporters chanted "Denver, Denver" - implying the Clinton-Obama contest will drag on until the convention - and "Madame President, Madame President".
Two women could be heard shouting at each other to "shut up".
An appeal for party unity was jeered by one heckler with the words "Lipstick on a pig!"
Puerto Rico votes on Sunday, followed by Montana and South Dakota on Tuesday - the last three Democrat primaries of the season.
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