One way to get around this, is to take more than one photo, and change the focus distance between them. The photos can then be merged in photo editing software, to yield one single photo where more than normal is in focus. This technique is some times referred to as focus stacking.
When having a lot of photos to merge, it is best to use some software to do the merging automatically, since it involves a lot of tedious, manual work. However, when only merging two photos, it can be done quickly in any photo editing software that feature layers, e.g., The Gimp.
Here is an example. I took this picture of two LEGO minifigures. The figures were placed in a simple macro soft box to get even lightning. I used the Panasonic Lumix Leica 45mm f/2.8 1:1 macro lens for the image, and placed the autofocus area on the figure faces for focus. I used f/5.6, which is far from enough from getting both figures in focus at the same time.
Photo 1: Left figure in focus:

Photo 2: Right figure in focus:

Merging the two images is a matter of loading them both into the same image in two different layers, and then removing the out of focus areas. Note that some lenses will give a different field of view depending on the focus distance. Hence, you may need to rescale one (or more) of the photos when merging.
This merged image would have been impossible to take with only one exposure:

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