In most cases the commission for your Buyer agent is paid by the listing agency.  Both agencies have agreed to this arrangement through their contract with the Multiple Listing Service (MLS). 

The Seller has already agreed to pay their agent a particular amount and the Seller's agent has agreed to split that amount with any agency which brings a buyer.  This is helpful to the Seller, and their agent, since it means there will be potential for a much larger pool of buyers looking at the property.

If the property you are interested in buying is not on the MLS, for example a For Sale By Owner property, then you will need to have a written agreement with your agent as to how you will be compensating them.  Typically the agreed upon commission will be written into the Purchase and Sale Contract in such a way that you can include it in any mortgage that you might be obtaining.  This allows for paying your agent at closing with no out of pocket expense to you.

It should be pointed out that no matter who is paying commissions on paper the Buyer is always paying any and all commissions by virtue of the fact that the Buyer is the one who brings all the money to closing.  If the Seller is "paying" commissions it is part of what they are getting paid for the property.  The Seller has figured that into what they accepted as payment on their property.  What the Seller is most interested in is what they "net" from the sale.  In essence the Buyer gets to pay a larger mortgage so that the Seller can "pay" the commissions.