Of course, "What is the single most important invention of the past two thousand years?" is one of those questions that does not really have an answer, like "What is the best novel/symphony/movie?
But if I had to make a choice, it would be the Hindu-Arabic number system, which reached essentially its present form in the sixth century.
Without it, Galileo would have been unable to begin the quantificational study of nature that we now call science. Today, there is scarcely any aspect of life that does not depend on our ability to handle numbers efficiently and accurately. True, we now use computers to do much of our number crunching, but without the Hindu-Arabic number system we would not have any computers.
Because of its linguistic structure, the Hindu-Arabic number system allows humans who have an innate linguistic fluency but only a very primitive number sense to use their ability with language in order to handle numbers of virtually any useful magnitude with as much precision as required.
In addition to its use in arithmetic and science, the Hindu-Arabic number system is the only genuinely universal language on Earth, apart perhaps for the Windows operating system, which has achieved the near universal adoption of a conceptually and technologically poor product by the sheer force of market dominance. (By contrast, the Hindu-Arabic number system gained worldwide acceptance because it is far better designed and much more efficient, for human usage, than any other number system.)