Atletico exploit the vogue for possession, so theoretically the best way to counter them is to force possession onto them, to draw their defence out. (According to match stats, Bayern had nearly 70% of possession.) But then possession based teams aren't usually best equipped to sit deep for any sustained period. Although in terms of personnel available, I'd say Bayern are a team that can play both. In fact the speed they have makes them perhaps even better suited to counterattack.
An interesting article I found re Simeone's tactics vs Mourinho's
http://theinsidechannel.com/guide-at...diego-simeone/