Just out of curiosity, listing the games mentioned here as of this writing by their date of release:

I love STALKER with all my heart, and if we're talking atmosphere and vibes and even world building it is up there. But it does not really belong in the objective masterpiece category. Flawed masterpiece, maybe.

Also I think Call of Pripyat is the better STALKER game, but it might be controversial.

I remember trying the demo to Homeworld when I was a kid, it came with one of those old school PC GAMER demo CDs. I think I was too young to understand how to play it effectively, but still loved it because I found the ambience of the experience so memorizing while hyper-cozy. Would you say it she's well as something worth going back and playing now, and what of the sequel(s)?

Prey, System Shock 2, Outer Wilds, and Undertale are fully-realized microcosms where the primary game is unfolding the complex origami of the setting. All of them absolutely beautiful to experience.

Supergiant games' holy trinity: Bastion, Transistor and Pyre.

Also, the only Borderland games 1 and 2; don't believe the lies there are no more true Borderlands games and no there most certainly is no movie.

There's also one other, but you'll need a crowbar or a gravity gun in hand for me to tell you about it.

Clair Obscur: Expedition 33
Disco Elysium
Alpha Centauri
Super Marios Bros 3
Bloodborne
Ori 1 & 2
Fallout 1 & 2
Planescape: Torment
The Outer Wilds

Do you think Return of the Obra Dinn would belong alongside these or is that game too flawed by comparison? I ask because I myself am not sure.

Oh, actually Disco Elysium would fit right in here as well as a "fully-realized microcosms where the primary game is unfolding the complex origami of the setting".

Historically a masterpiece has been a (or the) work that demonstrates an artist is capable of utilizing their medium to its fullest extent, i.e. it has been mastered. Per ye olde Wiki:

Historically, a "masterpiece" was a work of a very high standard produced by an apprentice to obtain full membership, as a "master", of a guild or academy in various areas of the visual arts and crafts.

In that light, I'd say the best qualified would be games that completely utilized the capabilities of the platform they were designed for or, perhaps of interest to more people, expanded what everyone thought could be done with those systems. Games which were furthermore well polished and complete, and did not have much room for improvement taking into account the constraints they had to work with at the time. (For instance: No duh we could make Mario 64 run at a higher framerate and have better textures to look nicer on hardware now. That doesn't mean it wasn't arguably a masterpiece of its time, on the system it was on.) This doesn't just have to be technical stuff -- It could be the way the game used storytelling, its gameplay mechanics, or anything else.

Have you played Prey? Only other game to scratch that same itch for me.

Nioh 2 is one of my favorite soulslikes, but falls short of masterpiece in my opinion due to the repeatedly recycled levels.

RDR2. Witcher 3. Fallout New Vegas.

Fallout 2

Wasteland 3.

Curious to hear what the criteria for "masterpiece" is, otherwise I think it is just peoples' subjective opinion of what makes a great game that they also think others might agree about being a great game. Genuinely curious, interested in discussion, not saying this to shut down any of the answers here.