The court ruled 4-1 against Skakel's request, saying the evidence doesn't back up the alternate claim.
Skakel - a nephew of Robert Kennedy's widow, Ethel - was sentenced to 20 years to life in prison in 2002 for fatally beating Martha Moxley with a golf club in a wealthy Connecticut suburb.
Prosecutor Susann Gill said she was pleased with the ruling denying Skakel a new trial and "hopefully sparing the Moxley family any further ordeal."
Skakel's attorneys, Hope Seeley and Hubert Santos, said it was a "travesty" that Connecticut courts won't allow a jury to evaluate the evidence.
"Fairness and justice require no less," they said in a statement.
Seeley told The Associated Press she will file another appeal in the coming weeks arguing Skakel had ineffective legal counsel when he was represented by Michael Sherman. Seeley has said Sherman failed to fully investigate witnesses because he had financial difficulties, a claim Sherman denies.
Skakel, 49, sought a new trial after Gitano "Tony" Bryant, who attended the same private school as Skakel, implicated two friends in the killing. A judge turned down that request in 2007, and Skakel then appealed to the state's highest court.
Bryant gave a videotaped statement to an investigator hired by Skakel in which he said his two friends were in Greenwich the night Moxley was killed. He said they told him they got Moxley "caveman style."
Bryant has since invoked his Fifth Amendment right against self-incrimination and declined to comment when contacted Monday by the AP. The two men he implicated have done the same.
Prosecutors have said Bryant's claim was fabricated and that nobody saw him and his friends in the predominantly white, gated neighborhood the night of the murder. Bryant and one of the men he implicated are black; the other has been described as mixed race.
The high court agreed with the trial judge and prosecutors that no one recalled seeing Bryant or his friends in the neighborhood that night.
"These three young men did not look like the average fourteen or fifteen year olds who would have blended into the crowd, particularly not in an area that was described by one witness as 'a fairly lily-white community,"' Justice Joette Katz wrote for the majority.
Furthermore, Bryant's account of his friends picking up golf clubs that night did not match the evidence, the high court said, saying that while golf clubs were found inside Skakel's house, no one reported seeing golf clubs lying in the Skakel yard on the night of the murder.
"There is no evidence, independent of Bryant, to corroborate any significant aspect of his account of the events of the night of Oct. 30, 1975, whereas there is a plethora of evidence to contradict his account," Katz wrote.
The court also questioned Bryant's credibility. He initially made his claim to a friend while they discussed collaborating on a screenplay about the crime, the court noted. His account "may not have been the only time that Bryant lied to or misled these friends," the court said, citing his claims that he was an entertainment lawyer even though he wasn't licensed to practice law.
Two justices wrote a concurring opinion calling Bryant's account "inadmissible hearsay" that would not change the verdict.
Justice Richard Palmer was the lone dissenter.
"At the very least, it is likely that this new evidence, when considered in light of the state's thin case against the petitioner, would give rise to a reasonable doubt" about Skakel's guilt, Palmer wrote.
Palmer wrote that he believed the lower court failed to evaluate the significance of the new information. Under state law, new evidence only has to meet a "minimum credibility threshold" for a new trial to be required, Palmer wrote.
"The evidence that Bryant provided during the course of his lengthy and detailed video-recorded interview satisfies all of the requirements necessary for a new trial," Palmer wrote.
John Moxley, the victim's brother, said he was not surprised by the ruling or that another appeal was planned.
"There's no credibility to that story," Moxley said, referring to Bryant's account. "For a judge to think that perhaps there was is mind boggling to me."
To win a new trial, Skakel's attorneys would have to prove that new evidence not available before his conviction could have changed the verdict.
Skakel also challenged the credibility of a star prosecution witness, who testified that Skakel confessed to him when they attended a private boarding school. After Skakel's conviction, his attorneys found three men the classmate named as possibly being present for the confession, but none said they heard it.
The Supreme Court agreed with the trial judge that the three witnesses could have been found before the trial and that Sherman, Skakel's trial attorney, failed to exercise due diligence in finding the witnesses.
The high court also said Sherman did not do enough to obtain reports on earlier suspects compiled by investigators.
In 2006, Skakel lost an appeal before the state Supreme Court in which he argued, among other things, that the statute of limitations had expired when he was charged in 2000. He still has an appeal pending in federal court.