Los Merengues made it 24 matches unbeaten against their city rivals thanks in part to a marvellous free kick in the first half from their talismanic No. 7
Jose Mourinho gave Los Blancos' fans the opportunity to boo him on the pitch 40 minutes before kick-off, but was greeted positively by those supporters inside the stadium, despite coming under criticism for his side's poor start to the Liga campaign that saw them start this match eight points behind their city rivals.
It did not take long for his side to take the lead in the match, as Ronaldo made it 1-0 to the reigning Liga champions with an unstoppable free kick in the 16th minute, while Mesut Ozil added a second after the break to seal the win.
Atletico's in-form forward Radamel Falcao was allowed his first glimpse at goal in the seventh minute when he got the wrong side of Pepe, but the Madrid center back managed to regain his composure and knock the ball behind as the Colombian attacker pulled back his left foot to shoot from the a tight angle.
Despite being second-best in the opening exchanges the home side took a 1-0 lead in the 16th minute in emphatic fashion through Ronaldo. The Portugal international made Diego Simeone's men pay for Arda Turan's foolish handball 30 yards from the Atletico goal by hammering the resulting free kick past Thibaut Courtois and into the bottom corner.
Tempers began to flare as the first half wore on, with Madrid's Sami Khedira following Turan into the referee's notebook, and Falcao's strike-partner Diego Costa seemingly doing his best to join them by clattering into a number of challenges with Madrid's centre-back pairing of Pepe and Sergio Ramos.
Madrid nearly increased its lead to two from another set piece in the 37th minute when Xabi Alonso set up Ronaldo for a long-range effort but Courtois was able to keep the attacker's strike out on this occasion, diving brilliantly to his right to parry the ball away.
The home side was slightly fortunate to end the first half with eleven men on the pitch after Ramos caught Falcao with a stray elbow as the two tussled for possession right in front of the linesman, while Atletico's midfield duo of Gabi and Mario Suarez avoided bookings in the minutes before the break after both went in late on Ronaldo.
The 15-minute break failed to calm either team as the second half was punctuated by spats between players from each side, just as the first half had been.
A clumsy challenge from the away side's right back Juanfran resulted in another dangerously-positioned free kick for Ronaldo, and again Courtois was forced into making a smart stop low down to his right to keep the score at 1-0.
However, three minutes later Madrid did manage to increase its lead, courtesy of Mesut Ozil. Atletico's makeshift left back Cata Diaz was caught out of position after his teammate Miranda headed the ball straight into the path of Ronaldo, and the Madrid forward quickly sprayed a pass to Ozil on the right. The Germany international adjusted his body well to meet the ball on the half volley with his left foot, and his shot flew straight and true into the bottom left corner.
Ronaldo still had time to strike both the crossbar and the post as Madrid controlled the closing stages, in stark contrast to the sluggish start it had made to the match.
Mourinho's men remain in third place in La Liga despite their win tonight, but the gap between these two sides now stands at just five points, with unbeaten Barcelona a further six points ahead of Atletico.