How does entropy increase over time?

Your cells have a bunch of energy in well organized structures called sugars. By the time you finish shuffling, you have turned them into more disorganized CO2 and H2O. The amount of entropy reduced in the card deck is less than the amount of entropy increased in these molecules.

To organize the cards you have to give up energy by moving the cards around (your arms moving for instance). You will also generate heat $\delta Q$, and your internal entropy will increase, \begin{equation} dS_{\text{you}} > {\delta Q \over T}. \end{equation} Second law of thermodynamics is precisely the statement that the total entropy will increase, \begin{equation} dS_{\text{you}} + dS_{\text{cards}} > 0. \end{equation} So you can only reduce the entropy of the cards by increasing your own or your surroundings by a greater amount.