Simao Sabrosa and Jose Antonio Reyes had given the nine-times cup winners a comfortable 2-0 half-time lead before Uruguay striker Forlan crowned a convincing win with two spot kicks in the second half.
On Wednesday, the 2007 winners Sevilla made the most of home advantage to establish a 2-0 first-leg lead over Getafe.
The return legs are next week.
Atletico, one of La Liga's most inconsistent sides, had already hit the post at a corner when Portugal winger Simao lashed home a spectacular volley from a Sergio Aguero cross in the ninth minute.
Racing had been unbeaten since the turn of the year but had struggled to create much danger and just before the break they failed to deal with Simao's low cross allowing Reyes to stroke home the second.
Simao hit a free-kick against the upright after the re-start and in the 63rd minute Jurado was brought down for the first penalty, though television replays showed the foul had happened outside the area.
Aguero had been tormenting the Racing defence all evening, and forced another penalty when he was upended as he dribbled towards goal in the 72nd minute.
Forlan made no mistake from the penalty spot once again, and Atletico were guilty of some wasteful finishing near the end.
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