Without sufficient light, the phase detect AF in most DSLRs really won't function. Essentially, the camera takes light and splits it to two different sensors. It uses the differences in the scene to determine focus. If there is not enough light to determine differences, you won't get autofocus.
In the field, I handle this in one of two ways:
1) I always carry a flashlight, that I use to light the scene to establish focus: Point your flashlight at the subject (or area), allow your camera to establish focus, then switch to Manual focus. (I am assuming you are using a tripod). This will maintain focus on your area of interest. (turn off the flashlight when done of course)
2)Turn on LiveView, then switch to Manual Focus. Zoom in with LiveView, and using the view on the LCD, adjust focus until you achieve a sharp image. Leave camera in Manual focus, but turn off Live view.
When a subject enters your pre-focused area, shoot away. Note that moving your camera will of course, likely result in images out of focus.