Former Porto striker Radamel Falcao fired the hosts ahead in the first half. He then added Atletico's fourth following goals from Miranda and Adrian after the break. Meanwhile, Jonas and Ricardo Costa scored for the visitors at the end of either half.
"The team showed their best side," Simeone told AS. "[We] were aggressive at all times.
"The win is not decisive, but it's a result that we all would have taken beforehand.
"We will go to Valencia knowing it will be tough, in a great atmosphere."
The Spanish outfit are scheduled to host Espanyol in La Liga on Sunday.