Yes, they held just what you quote them as having done, which is not what the article says they held. The article claims that the court ruled that "human genes cannot be patented, though synthetic DNA, created in the laboratory, can be". While the court did enunciate a principle that could be summarized in that way, and did follow that principle in its first holding, which invalidated some of Myriad's patents, it violated that principle in its second holding, in which it validated two of Myriad's patents of human genes.
The principle is that human genes are not patentable because they are discovered in nature, not invented by a human being, and allowing them to be patented would violate the fundamental point of patent law, whereas synthetic genes, as human inventions, are patentable. But they failed to correctly apply that principle in their second holding. The cDNA representations of the human genes BRCA1 and BRCA2, which are what Myriad had patented, were simply not invented by Myriad -- they were copied, letter-for-letter, from the gene as represented in naturally occurring mRNA. The court fell into the same mistake that the lower court they criticized in the first holding had made: failing to recognize that copying is not inventing. So the court did not in fact rule as the article stated.