"Such families must cope every day with tremendous challenges in caring for their autistic children, and all are deserving of sympathy and admiration," special master George Hastings Jr., wrote.
But, he added, Congress designed the victim compensation program only for families whose injuries or deaths can be shown to be linked to a vaccine and that has not been done in this case.
The ruling came in the so-called vaccine court, a special branch of the U.S. Court of Federal Claims established to handle claims of injury from vaccines. It can be appealed in federal court.
Friday's decision that autism is not caused by thimerosal alone follows a parallel ruling in 2009 that autism is not caused by the combination of vaccines with thimerosal and other vaccines.
The cases had been divided into three theories about a vaccine-autism relationship for the court to consider. The 2009 ruling covered one theory, and a second was dropped after that. Friday's decision covers the last of the three theories.
That doesn't necessarily mean an end to the dispute, however, with appeals to other courts available.
The new ruling was welcomed by Dr. Paul Offit of Children's Hospital of Philadelphia, who said the autism theory had "already had its day in science court and failed to hold up."
But the controversy has cast a pall over vaccines, causing some parents to avoid them, he noted, "it's very hard to unscare people after you have scared them."
On the other side of the issue, a group backing the parents' theory charged that the vaccine court was more interested in government policy than protecting children.
"The deck is stacked against families in vaccine court. Government attorneys defend a government program, using government-funded science, before government judges," Rebecca Estepp, of the Coalition for Vaccine Safety said in a statement.
SafeMinds, another group supporting the parents, expressed disappointment at the new ruling.
"The denial of reasonable compensation to families was based on inadequate vaccine safety science and poorly designed and highly controversial epidemiology," the goup said.
The advocacy group Autism Speaks said "the proven benefits of vaccinating a child to protect them against serious diseases far outweigh the hypothesized risk that vaccinations might cause autism. Thus, we strongly encourage parents to vaccinate their children to protect them from serious childhood diseases."
However, while research has found no overall connection between autism and vaccines, the group said it would back research to determine if some individuals might be at increased risk because of genetic or medical conditions.
Meanwhile, in reaction to the concerns of parents, thimerosal has been removed from most vaccines in the United States.
In Friday's action the court ruled in three different cases, each concluding that the preservative has no connection to autism.
The trio of rulings can offer reassurance to parents scared about vaccinating their babies because of a small but vocal anti-vaccine movement. Some vaccine-preventable diseases, including measles, are on the rise.
The U.S. Court of Claims is different from many other courts: The families involved didn't have to prove the inoculations definitely caused the complex neurological disorder, just that they probably did.
More than 5,500 claims have been filed by families seeking compensation through the government's Vaccine Injury Compensation Program, and the rulings dealt with test cases to settle which if any claims had merit.
Autism is best known for impairing a child's ability to communicate and interact. Recent data suggest a 10-fold increase in autism rates over the past decade, although it's unclear how much of the surge reflects better diagnosis.
Worry about a vaccine link first arose in 1998 when a British physician, Dr. Andrew Wakefield, published a medical journal article linking a particular type of autism and bowel disease to the measles vaccine. The study was later discredited.