Em /etc/yum.conf
set installonly_limit=3
. Citando a documentação :
installonly_limit Number of packages listed in installonlypkgs to keep installed at the same time. Setting to 0 disables this feature. Default is ’0’. Note that this functionality used to be in the "installonly" plugin, where this option was altered via. tokeep. Note that as of version 3.2.24, yum will now look in the yumdb for a installonly attribute on installed packages. If that attribute is "keep", then they will never be removed.