Well, typically one doing re-keying work on wafer locks would have a set of replacement wafers to use, but I'm probably getting ahead of myself.
First things first. Can you put your car key in the fuel lock? (IE, is it the same keyway.)
Most gas cap locks I've seen are not compatible with the car key, but if yours is, then you're in luck, it can be re-keyed to your car key.
The proper way to do this is to either get a wafer re-keying set, so you can replace the wafers with ones that fit your car key, or take it to a locksmith who has one for him to do. (the latter would likely be the cheapest plan about $10-15)
I'd advise against filing the wafers down to fit as that would make the lock less secure, by putting a much greater variance in the tolerance of the lock, and possibly allowing other keys to turn it.
Another possibility I've done before, also decreases the security of the lock, but if you're just concerned about a minor hindrance to unauthorized opening it may work. Put your car key in the lock and see if that places any of the wafers flush with the plug, (The proper open location) if so, take the wafers that are at the locked elevation out, and try switching them around to different locations on your key. Basically you're re-keying the lock with the same wafers it had, just in a different order. The problem here is it's unlikely more than one or two wafers would fit properly on your key. So in effect it'd be a 2 wafer lock, which is absurdly easy to pick.
Really the best/most secure option is to either get a wafer set to do it properly, or get a locksmith to do it.
If on the other hand your car key does not fit in the fuel lock keyway, you're out of luck