Talos Principle and The Witness. Just Cause 2 even though it's got enemies all over the map, just by virtue of how large the game world is. GTA V gave me a refreshing feeling of isolation when I played it years ago, purposely flying off into the distant horizon away from all of the chaos and action, or just wandering the wilderness. Minecrap on peaceful mode, especially with some environment enhancing mods.
I'm sure there are a plethora of games like you describe if you simply search a tag like "environmental" or "atmospheric," but I don't think they would give the same feeling, since they're designed for that specific element. The sort of experience exploring a game world or the wilderness always means more when you know it wasn't the main intent of the game devs. It makes your action feel like actual exploration into some unknown territory. WoWin the day and things like finding the little attention to detail secrets in The Elder Scrolls made me feel that way, anyway.