If you did not fall short in looking after the money or in staying in the store and keeping an eye on what was in it, then there is no blame on you. You have to tell the owner of the store. That may be better than him finding out by himself that that money is missing. All you have to do is delegate your affairs to Allaah, may He be glorified and exalted, and trust that He will show you to be innocent.
But if what happened was because of neglect on your part, then you have to pay back the money to the owner of the shop, unless he lets you off.
And Allaah knows best.