The "Base-Path" for Mysql is stored in /etc/my.cnf
which is not updated when you do brew upgrade. Just open it and change the basedir value
For example, change this:
[mysqld]
basedir=/Users/3st/homebrew/Cellar/mysql/5.6.13
to point to the new version:
[mysqld]
basedir=/Users/3st/homebrew/Cellar/mysql/5.6.19
Restart mysql with:
mysql.server start