As noted by Riedsio, the session variables do not change after connecting unless you specifically set them; setting the global variable only changes the session value of your next connection.
For example, if you have 100 connections and you lower the global wait_timeout then it will not affect the existing connections, only new ones after the variable was changed.
Specifically for the wait_timeout variable though, there is a twist.
If you are using the mysql client in the interactive mode, or the connector with CLIENT_INTERACTIVE set via mysql_real_connect() then you will see the interactive_timeout set for @@session.wait_timeout
Here you can see this demonstrated:
> ./bin/mysql -Bsse 'select @@session.wait_timeout, @@session.interactive_timeout, @@global.wait_timeout, @@global.interactive_timeout'
70 60 70 60
> ./bin/mysql -Bsse 'select @@wait_timeout'
70
> ./bin/mysql
Welcome to the MySQL monitor. Commands end with ; or \g.
Your MySQL connection id is 11
Server version: 5.7.12-5 MySQL Community Server (GPL)
Copyright (c) 2009-2016 Percona LLC and/or its affiliates
Copyright (c) 2000, 2016, Oracle and/or its affiliates. All rights reserved.
Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective
owners.
Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.
mysql> select @@wait_timeout;
+----------------+
| @@wait_timeout |
+----------------+
| 60 |
+----------------+
1 row in set (0.00 sec)
So, if you are testing this using the client it is the interactive_timeout that you will see when connecting and not the value of wait_timeout