Just started a low-magic game with my group. So far we're addressing it purely with game fiction and things are going well. The most important thing we did to achieve this was discussing the fictional world we wanted up front and agreeing to play to that fiction.
What came out of our discussion was basically this:
-Magic is rare; those who can bend magic to their will are rare
-Magic is powered by dark, difficult to control, and ultimately corrupting forces
-Practical magic items are non-existent; relics and strange artifacts of power exist but are rare and dangerous
-Those wielding magic are feared and distrusted by ordinary folk. It's not a respectable thing to dabble in at best. At worst, it's torches and pitchforks time.
-And we decided to not have any clerics. Plenty of weird gods, shammans, cults, etc. But no walking hit point battery in chain mail. This required a small mechanical tweak. So far I'm going with "At the end of a Scene, you heal equal to 1/2 your Constitution." Still testing this mech out, though.
So far the party has one wizard, and he's role-playing the hell out of how and why his magic works. His magic missiles are invisible mental blows that batter his targets minds. When he casts a light spell, he must pull it down from a true light source and "capture" it. Casting fails have unpleasant consequences, due to the source of his power. He's constantly scrounging for strange spell ingredients, creeping out the other members of his party. And, most importantly, he's not hurling spells left and right. He keeps a low profile, because... pitchforks and torches.
The party also has a Paladin. He has yet to lay on hands. When he finaly does, I'm sure it will be interesting. I doubt he will select any of the Paladin casting moves, but if he did, I'm sure we could work it into the fiction.
So that's all a really long winded way of saying "follow the fiction." It really does work well. Just discuss the world you all want to play in up front. The more everyone feels like they had a hand in laying the foundation, the more enthusiastic they'll be in building on it.
All that said-
If you want a solid mechanical fix for spells, then noofy's suggestion to use the Monster of the Week magic rules would be a good start. That's the direction I was headed initially, but laziness prevailed. If you want to develop some custom low-magic char sheets, I'd love to see them!