The collaboration uses artificial intelligence to map the site, and augmented reality to help restore the original home of the Olympic Games.
It will allow viewers to explore the area as it stood more than 2,000 years ago.
Microsoft has ambitions to rival Facebook with its own plans for the so-called metaverse.
It recently announced Microsoft Teams metaverse for meetings and is keen to transform Minecraft and other games it owns into more immersive 3D worlds.
Its tie-up with the Greek government means people can tour the site remotely or in person with an augmented-reality mobile app. At the Olympic Museum in Athens they can use HoloLens headsets to overlay a digital version of the site.
Microsoft's augmented reality smart glasses HoloLens use multiple sensors, advanced optics, and holograms, to display information, blend with the real world or simulate a virtual world.
Among the 27 monuments to be preserved are the original Olympic Stadium, the temples of Zeus and Hera, and the workshop of the renowned sculptor Phidias.
The buildings are as close as possible to their original forms and include historical timelines of the site's changes over time, and depictions of artefacts from each period.