Actually not. The copy now on display has three commas, but the original one sent from Congress to the printer and at least some of those sent to the states for ratification had only one. The one between the two phrases "A well regulated Militia being necessary to the security of a free State," and "the right of the people to keep and bear arms shall not be infringed.". It's a long sentence and if you speak it you may have a tendency to pause at the location of the other two commas, that's all they indicate, whereas the comma separating the two phrases does exactly that. The first (dependent) phrase is a sort of preamble, giving a reason "why", the second (independent) phrase tells "what". The dependent phrase does not restrict the independent phrase's command.
Until fairly recently (in terms of the time since the Bill of Rights was passed) the printed versions were the single comma one. The surplus commas were not put there by Congress, and were not voted on by Congress or the States, they were put there by the printer/transriber. See the SAF site and Talk,Politics,Gun FAQ
In any event, three commas or only one, the command is clear "the right of the people to keep and bear arms(,)shall not be infringed".