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Start with one at a time, so a broken yolk doesn't ruin your whole plate. Keep a second bowl on the side for the yolks. Hold the bottle in this partially crumpled position. Place the mouth of the bottle on top of the egg yolk, and slowly release your grip. The air pressure will push the yolk into the bottle. This might take some practice; releasing too much or too quickly will pull up some of the egg whites as well. Carefully keep the bottle compressed so the yolk stays inside the bottle. Move the bottle over to the other bowl and let go to drop in the yolk. Tilting the bottle a little may help.
Carefully crack the egg onto a shallow bowl. Squeeze some of the air from a clean plastic bottle. Pick up the yolk. Transfer the yolk to the other bowl.