Apple scored a sweeping legal victory over its South Korean competitor in August when a U.S. jury found Samsung had copied critical features of the hugely popular iPhone and iPad and awarded Apple $1.05 billion in damages.
The 'pinch-to-zoom' patent, U.S. patent no. 7,844,915, was one of the patents contested at that trial. The jury ruled that Samsung had infringed six of seven Apple patents.
When the U.S. patent office rules against a patent, the full process involves multiple steps and can take years. It can also often be appealed in court, further tying up the process.
The ruling by the U.S. patent office after Samsung requested an examination of the patent was included in documents filed by Samsung in a federal court in San Jose, California.
Apple's claims were rejected on the grounds that prior patents covered the inventions.
Representatives for Apple and Samsung were not immediately available for comment.
Samsung and Apple, the world's top two smartphone makers, are locked in patent disputes in at least 10 countries as they vie to dominate the lucrative mobile market and win over customers with their latest gadgets.
In October, a Dutch court ruled that Samsung did not infringe on Apple's patent by using certain multi-touch techniques on some of the Samsung Galaxy smartphones and tablet computers.