The 33-year-old billionaire appeared in a virtual reality broadcast as a bobbing, grinning cartoon character against a backdrop of real-life footage from the stricken US territory.
At least 43 people died when Hurricane Maria struck the island last month and millions of people are still homeless or without essentials.
And Mr Zuckerberg was forced to apologise after the broadcast was roundly condemned on his own Facebook page as “tone-deaf” and “part disaster tourism, part product promotion”.
In the clip, which was watched more than 1.7 million times on Facebook, avatars of Mr Zuckerberg and his company’s head of social virtual reality, Rachel Franklin, “teleport” to the Puerto Rican disaster zone.
Mark Zuckerberg’s avatar on virtual reality trip to Puerto Rico
I’m sorry to anyone this offended
As they move into a flooded town, standing in front of people’s wrecked homes, Mr Zuckerberg says: “One of the things that’s really magical about VR is you can get the feeling you’re really in a place.
“Rachel and I aren’t even in the same building in the physical world, but it feels like we’re in the same place and can make eye contact.”
He went on to explain how Facebook was helping with disaster relief, including donating £1.13 million and working with the Red Cross to build “population maps” so relief teams know where the most help is needed.
Mark Zuckerberg VR broadcast was described as heartless and ‘tone-deaf’
Ms Franklin says: “You can see that we can really feel like we’re here.”
Mr Zuckerberg adds: “This street is really flooded.”
The pair then “teleport” back to Facebook’s California HQ and continue their broadcast by promoting the company’s upcoming Oculus developer conference by showing a 360-degree video from the 2016 event.
Posing in front of hurricane-wrecked homes upset readers
Mr Zuckerberg later issued and apology for the Puerto Rici stunt after criticism on his Facebook profile.
He said: “One of the most powerful features of VR is empathy.
“My goal here was to show how VR can raise awareness and help us see what’s happening in different parts of the world.
“Reading some of the comments, I realise this wasn’t clear, and I’m sorry to anyone this offended.”