Raul Garcia opened the scoring in the 17th minute as he rose unchallenged to head Gabri's cross home.
It was 2-0 only four minutes later when Diego Costa just managed to finish past Rayo goalkeeper Cobeno after Arda Turan's cut-back.
Costa turned goal-scorer on 35 minutes when he fed Arda, who took the ball around the keeper and found the empty net.
Gabri sprung the Vallecano offside trap to head home eight minutes into the second half before Garcia completed his brace in the 90th minute with a tap-in.
The victory lifted Atletico to their second straight win of the season while Rayo will be disappointed after a 3-0 win against Elche on the opening day.Meanwhile, Celta Vigo secured their first win of the season as they overcame Real Betis 2-1.
All goals were in the second-half with Charles and Nolito establishing a two-goal lead for Celta before Ruben Castro scored a consolation for Betis on 90 minutes.
And Levante recovered from the seven-goal loss to Barcelona on the opening weekend of the season with a 0-0 home draw against Sevilla, with Sergio Pinto spurning the best chance of a drab encounter when he fired into the side-netting when through one-on-one in the first half.