Maybe make the ability require an upgrade, then when the hero reached X level, set the upgrade to finish so that the hero can use the ability. But the "upgrade complete" message would come up and it'd look ugly.
Another is to make two versions of the ability, one requiring an upgrade and one that don't require an upgrade. The hero starts off with the ability which requires the upgrade, but when the hero reaches X level, replace the ability that needs the upgrade with the other one which requires no upgrade.