The Caribbean island territory, which does not have the right to vote in November's presidential election, was holding the third-last contest of the primary season heading to Tuesday's climax in Montana and South Dakota.
The Democratic Party's decision Saturday to reinstate delegates from Michigan and Florida, but with their voting power halved, put Obama, 46, two giant strides closer to making history as the first black presidential nominee.
But on a day of drama Saturday, Obama also took a heavy political hit, announcing he would quit his Chicago church, which has seen preachers fire off a string of racial rhetoric that rocked his campaign.
The Florida and Michigan compromise saw delegates apportioned to both candidates and scuppered Clinton's hopes of making a significant dent in her rival's lead in the race to take on Republican John McCain.
The decision moved the finish line for the Democratic nominating contest up to 2,118 delegates, with Clinton gaining a net 24 delegates from the two-state compromise struck at a stormy meeting in Washington.
That left Obama within 66 delegates of the target before Puerto Rico's votes are counted.
A total of 86 pledged delegates are on offer in Puerto Rico, Montana and South Dakota. There are also nearly 200 "superdelegates" or top party officials who are yet to declare their allegiance.
Puerto Rico will award 55 pledged delegates, and Clinton was leading Obama in the territory 55 per cent to 42 per cent, according to a poll cited by The Washington Post.
Saturday's meeting of the Democratic National Committee's rules and bylaws panel was called to rule on the fates of Florida and Michigan, which broke party rules by holding their primary votes in January.
Clinton won both unofficial contests, though neither candidate campaigned in Florida, and Obama was not on the ballot on Michigan.
Top Clinton aide Harold Ickes complained the committee had "hijacked" four delegates from Clinton in Michigan, and said the campaign may challenge the ruling ahead of the party's August nominating convention.
Some Clinton backers chanted "McCain, McCain," saying they would vote for the Republican nominee, and screamed "Denver, Denver," to demand a convention challenge.
But Obama said he believed in the patriotism of Senator Clinton and her husband, former president Bill Clinton, and their loyalty to the Democratic cause.
"They love the Democratic Party. I think they deeply believe that Democrats need to win in November," Obama said. "And so I trust that they're going to do the right thing."
The committee voted 19 to 8 to restore Michigan, after earlier voting 27-0 to reinstate Florida.
Clinton will get 69 delegates in Michigan, who will each only have half a vote in nominating the party's presidential nominee. Obama will get 59 delegates.
In Florida, Clinton will get 52.5 delegates to Obama's 33.5, again with each delegate only getting half a convention vote.
Clinton spokesman Howard Wolfson said on Fox News Sunday that the former first lady was ahead in the popular vote and had bested Obama in key swing states.
"That's a strong argument that Senator Clinton would be the best nominee against Senator McCain," he said.
But David Bonior, an Obama supporter and former congressman from Michigan, said: "The rules are based on delegates, not on popular votes."
Obama announced his decision to leave the Trinity United Church of Christ almost a week after guest preacher Father Michael Pfleger launched a mocking, racially tinged attack on Clinton.
Trinity's former pastor was Reverend Jeremiah Wright, who sent the campaign into turmoil when videos emerged of a string of vehement, race-based sermons emerged earlier this year.
"This is not a decision I come to lightly, and frankly it is one I make with some sadness," Obama said, but he had concluded "it was going to be very difficult to continue our membership there so long as I was running for president."