Los Blancos and Kylian Mbappe may have struggled in Europe this season, but the Frenchman looked bright from the start, collecting Brahim Díaz's pass before firing into the bottom corner just ten minutes in for his 50th Champions League goal.
Shortly afterwards he raced through again before seeing a venomous attack blocked by Marco Carnesecchi.
Ademola Lookman asked questions at the other end, with a shot blocked by Aurelien Tchouameni and a low cross for Charles De Ketelaere forcing a crucial intervention from Antonio Rudiger.
Wderson became the last player to have a shot blocked by Tchouameni and Lookman hit wide as La Dea stepped up their search for an equalizer.
There was early disappointment for Real Madrid, however, as Mbappe was sent off injured in the 36th minute before Rudiger headed wide after a golden opportunity to double his side's lead.
The centre-back's frustrations were compounded when his partner Tchouameni Sead tripped Kolasinac and conceded a penalty which De Ketelaere emphatically converted with the final kick of the half, especially as the German had previously exchanged heated words with the striker.
Buoyed by that moment, Atalanta showed intent after the restart, with De Ketelaere rising above Rudiger but heading wide before Lookman forced Courtois into a save with his strike from distance.
However, they fell behind in the 57th minute when the ball bounced off Ederson and happened to fall to Vinicius Junior, who made the most of it with a clinical finish.
Just three minutes later, Jude Bellingham cut inside Marten de Roon and beat Carnesecchi to give his side a cushion.
Lookman was quick to remind that Atalanta were not out of the game yet, smashing his shot through the legs of Lucas Vazquez and out of Courtois' reach.
Diaz and Rodrygo each squandered a chance to regain some breathing space, but Courtois denied substitutes Lazar Samardzic and Mateo Retegui before the latter missed the target after a golden chance as Real Madrid secured a crucial win in response to their previous back-to-back back Champions League defeats, currently 18th in the standings.
They also inflicted Atalanta's first European defeat this season, although La Dea are still currently in ninth place.
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