The home side were rocked back in the second minute when Ronaldo sped down the left wing, cut inside and struck with a low shot from just outside the penalty area for his fifth league goal in four matches.
Villarreal defender Gonzalo Rodriguez was sent off 10 minutes before the break, earning a second yellow card for catching Kaka in the chest with a reckless flying kick.
Kaka stepped up to double Real's lead in the 73rd minute when the referee ruled Angel Lopez had handled Marcelo's cross and Gonzalo Higuain and Ronaldo both went close as Real pressed for a third.
Ronaldo scored inside the first minute in Sunday's 5-0 rout of promoted Xerez and he said his early goal on Wednesday had thrown Villarreal off their stride.
"They are difficult to beat at home but we managed it and after Kaka's goal we were more in control," he told reporters.
Piatti then grabbed his second to secure a point for Hugo Sanchez's side and Atletico's players and staff were whistled from the pitch by their disgruntled fans.
