There is no save for Stone to Flesh. A Stone Golem has no ability that allows it a save against the spell. It does have a specific weakness to the spell that tells you how it effects the creature however.
So instead of becoming an inert piece of flesh, the Golem loses Golem Antimagic and it's resistance to physical damage for one round.
It could still be helpful to say that IF the spell had featured a save, the Golem would get to save.
It would not get a save. Golems are only effected by magic in the ways that their Golem Antimagic states they are. Hence why a golem with a weakness to fire doesn't make a save against a Fireball, it just takes the damage as is.
Any magic of this type that targets the golem causes it to take the listed amount of damage (this damage has no type) instead of the usual effect. If the golem starts its turn in an area of magic of this type or is affected by a persistent effect of the appropriate type, it takes the damage listed in the parenthetical.
You don't have to roll to hit a golem with magic, and they do not make saves against it. They simply take the listed amount of damage, or whatever other effect is called for.