Okami. Fire burns trees and ice, as well as lights torches. Water extinguishes fire and fills containers. Wind moves round objects, blows out fire, moves fans, and affects enemies. Then there are slashing maneuvers, bombs, sprouting trees, time dilation, changing the time of day by moving the position of the sun/moon or swapping them out... And these are all physics that can be used at any point in the games limited open world.
No, it isn't as organic as BotW, but it's also, what, ten years older?
Okami is a great game, but as Chrkeller points out, most of those are canned gameplay mechanics, not dynamic physics/chemistry as such.