People typically use a beer gun for this. It has the ability to purge the bottle with CO2 and then slowly fills the bottle with beer. The slow fill and the flow path are both designed to keep as much CO2 as possible in solution so the beer stays carbonated.
You can also use a counter pressure filler which is similar but instead of slowly filling up the bottle at normal atmospheric pressure it actually pressurized the bottle so the beer stays under pressure until you remove the filler.
Both systems give good results. The beer gun is a bit simpler to use and also a bit more expensive.