Let me define 2 and 3-tier architecture first in very simple terms, cause that's how I know them.
2-tier: A client that connects directly to a database.
3-tier: A client connects to a business logic layer that connects to the database.
Now you can use PHP to build both 2 and 3 tier systems it all depends on what architecture works best for you.
Most PHP database applications are 2 tier. People connect to the web page and the PHP script there gets information directly from the database or puts it directly into the database.
You can however user PHP as the client and have it connect to a business logic layer instead of the database. This layer can be written in whatever you want, even PHP, all it does it manage ways for data to get from the database to the client and vise versa. This takes some of the power away from the client, but it also removes some of the headaches since the client doesn't need to know what the database is or how to connect to it. And you business logic layer doesn't need to know what the proper formatting of the data should be for the user to read it, it just has to worry about serving up the data.