A couple of things:
1. The pre-flash doesn't help, however a Speedlight can project a red target on the subject, giving the camera's AF system something to "see."
2. Set the AF system to "One Shot" or "Single" rather than Continuous or "A.I." Not only does this activate the AF target from your speedlight, but it's more accurate in dark conditions.
3. If your camera has a "live view" option, you could use that setting, zoom in on the LCD screen, and manually focus on the subject. Then turn off live view and shoot.
All of this presumes that your subject is not moving.
May be a laser pointer that can communicate to the camera+lens will be great.