Los Blancos claimed a morale-boosting 1-1 draw at Barcelona in the Copa del Rey semi-final first leg in midweek and they produced another resilient display to beat Diego Simeone's men on their own turf for the first time since their meeting at Vicente Calderon in November 2016.
Atletico conceded twice in a first half at the Wanda for the first time, as Sergio Ramos's penalty added to Casemiro's spectacular opener after Antoine Griezmann had equalised, with a little thanks to the video assistant referee (VAR).
Madrid looked in control at the back under pressure in the second half and finished off its opponent 16 minutes from time through substitute Bale's landmark goal, before Thomas Partey's late sending off.
A fluid Madrid looked bright in the early stages and deservedly went ahead 16 minutes in, Casemiro producing a brilliant bicycle kick to beat Jan Oblak after Ramos nudged the ball on from a corner.
Atletico responded well and levelled nine minutes later, as Angel Correa contentiously robbed Vinicius Junior and fed Griezmann, who beat the offside trap and slotted through Thibaut Courtois's legs.
But Ramos restored the lead just before the break, confidently dispatching a penalty into the bottom-left corner after Jose Gimenez clumsily tripped Vinicius, with VAR adjudging it to have happened just inside the box.
Atletico thought it had equalised when Alvaro Morata lifted the ball over Courtois and into the net in the 54th minute, but VAR proved he was marginally offside.
Madrid took full advantage in the 74th minute, as Bale, who replaced Vinicius before the hour mark, raced on to Luka Modric's pass and fired across Oblak into the bottom-right corner.
Atletico's fate was sealed with 10 minutes remaining when Thomas received a second booking for catching Toni Kroos.