The former first lady's victory in the popular vote swung the final unallocated New Mexico delegate into her column, which gave Clinton 14 delegates in the state to 12 for Obama.
With the addition of New Mexico's delegate, the national delegate count stood at 1,276 for Obama and 1,220 for Clinton on Thursday.
"I am so proud to have earned the support of New Mexicans from across the state," Clinton said in a written statement. "New Mexicans want real solutions to our nation's challenges. As president, I will continue to stand up for New Mexico and will hit the ground running on day one to bring about real change."
The Obama campaign appeared to accept the outcome.
Obama's state director, Carlos Monje Jr., was asked Thursday if he was confident the results were 100 percent accurate and replied, "We have confidence in the process." Asked if Obama might seek a recount, he said Obama has momentum from eight wins since Super Tuesday and "we are going to look forward at the contests we have remaining."
Monje said there were some "troubling aspects" in the conduct of the caucus, including "incredibly long lines that kept people from voting," but he saw their solution in the future. "We're going to continue to work with the New Mexico Democratic state party to make sure the next election goes more smoothly."
Of the 22 states that held Democratic primaries and caucuses on Super Tuesday, New Mexico was the last to report a winner. The caucus here was run by the state Democratic party rather than by state government.
Colon, who came under fire for his handling of the troubled election, thanked the hundreds of volunteers who counted the ballots. The final figures "have been double and triple checked," he said in a televised announcement.
New Mexico Democrats call their contest a caucus, but it's not like Iowa's caucuses where voters gather in gyms, churches or meeting rooms, divide into groups for each candidate, try to attract more support from other groups, and then count each group.
Rather it more closely resembles a "firehall primary" - a primary with shorter voting hours and fewer voting sites than would be found in traditional state primaries.
It was a mess: Overwhelmed polling places with long lines, some up to three hours. Too few ballots. Confusion over where to vote.
Bad weather in the north. In Rio Rancho, one of the state's largest cities, a single polling location where 1,900 people remain lined up at 7 p.m on election night.
Colon has apologized repeatedly: "We absolutely miscalculated and I apologize. It's a tragedy when folks are not afforded the opportunity to vote."
The firestorm of criticism included some from Democratic Gov.
Bill Richardson, a former presidential hopeful who said he was "deeply disturbed" by the problems. Partly because he was a candidate himself until mid-January, Richardson himself never got involved in helping plan or promote the caucus, as he did in 2004, the first year New Mexico tried it.
On Super Tuesday, Clinton and Obama vied for 26 of New Mexico's 38 delegates to this summer's Democratic National Convention.
Twelve so-called superdelegates are not bound by caucus results.
New Mexico awards Democratic delegates proportionally, based on statewide vote totals and on the results in individual congressional districts.
In two of the state's three congressional districts, Clinton and Obama equally split an even number of delegates at stake. In District 2, which had an uneven number of delegates, Clinton won the additional one by outpolling Obama by 55 percent to 41 percent, according to unofficial results.
Nine statewide delegates were at stake. Obama and Clinton evenly split the eight delegates already awarded. The final one was assigned to the statewide popular vote winner.
