One way would be to check the player and enemy's Y-position on collision.
If the player's y-position is less than the enemy's y-position then it should that the player jumped on the enemy. Probably it needs some tweaks to work in some cases but it's a start.
Check out the demo project "Kiwi Story", it has the functionality you're looking for.
In Kiwi Story, Open the event sheet "eEnemies" and look at event 55 and event sheet "ePlayer" and event 35.