Ronaldo cleanly beat goalkeeper Victor Valdes in the 82nd minute for his first career goal against Barcelona after Daniel Alves was adjudged to have brought Marcelo down inside the area.
Messi scored his 49th goal of the season from the penalty spot in the 53rd to put the visitors ahead at Santiago Bernabeu Stadium after Madrid defender Raul Albiol was red-carded for tugging striker David Villa down inside the area.
Madrid scored points against its biggest rival for the first time in six games but remained eight points behind the two-time defending champions with six rounds left.
“We're not champions yet with 18 points still up for grabs,” said Barcelona coach Pep Guardiola.
Madrid was in danger of starting the first of four “clasicos” against its historic rival with defeat after Albiol's sending off deflated a first 50 minutes in which coach Jose Mourinho's defensive tactics had largely stymied the visitor's attack.
“Eleven against 10 and it was practically mission impossible. Especially against a team that — with possession of the ball — are the best in the world,” said Mourinho, who has faced Barcelona with one less player before as coach of Chelsea and Inter Milan. “I'm tired of having to prepare for Barcelona games with 10 men.” While the result was unlikely to improve its chances of denying Barcelona a third straight league trophy, Madrid can go into Wednesday's Copa del Rey final at Valencia with momentum after erasing memories of November's 5-0 loss at Camp Nou. The two Spanish giants still have a two-leg Champions League semifinal to play.
“You always learn something for the next game. We will learn what we have to do to attack a little bit better,” Guardiola said. “We should have attacked Casillas' goal more when it was 1-0 but its natural to sit back some when you're in the lead.” Even the normally diminutive Messi let out a cry of “Vamos!” (“Let's Go!”) after scoring the opener, his league-leading 30th goal that moved him one shy of becoming the first Spanish league player to reach the half century mark. It was the Argentina international's first goal against Mourinho-coached clubs.
Mourinho looked to frustrate Barcelona with a block of defensive players in the center of his lineup, and it largely worked as Barcelona was often forced to backpedal under pressure with Messi the only Barcelona player able to penetrate the area in the first half.
Messi, whose 19th-minute chip was stopped by Casillas, darted across the area and, surrounded by four white shirts, managed to unleash a rising shot that Casillas saved in the 44th.
Moments after Barcelona's best effort of the half, Madrid replied with its own as Ronaldo — whose poor touch in the 34th erased a solo chance from inside the area — watched as Barcelona defender Adriano cleared his header off the line in the 45th.
Madrid's best chances were off counterattacks or set-pieces and Ronaldo again looked on in disbelief in the 50th after beating Valdes again only for his dipping free kick to come off the bottom of the post.
Villa's scoreless streak reached 10 games but his tussle with Spain teammate Albiol set up the goal and meant the Madrid defender misses the cup final after being shown a direct red card.
Mourinho replaced Benzema with Oezil after that while Barcelona captain Carles Puyol — playing for the first time since January because of a knee injury — came off with a slight muscle strain.
Xavi Hernandez curled a shot off the crossbar in the 64th as the Catalan side found more space to work with, but it was the hosts who created the better chances to the close as Pepe somehow bungled a chance in front of Valdes soon after.
Striker Emmanuel Adebayor's entrance in the 67th gave Madrid a large target up front and it nearly capitalized several times before Daniel Alves tripped up his fellow Brazilian for Ronaldo to score his 29th league goal and 40th of the season. Sami Khedira had an opportunity at the close, but shot straight at Valdes.
“We drew and nearly won but, with the circumstances of the game, it's a draw you have to be happy with,” said Mourinho, who believed Alves should have been sent off for a second booking for bringing down Marcelo.
Still, Madrid's players and the Bernabeu celebrated nearly as heartily as if it was a victory.
Earlier, Julio Baptista returned from injury to score twice as Malaga beat Mallorca 3-0 while Venezuela striker Miku lifted Getafe to a 1-0 win over Sevilla.
Also, Valencia moved nine points clear of fourth-place Villarreal with a 3-0 win at last-place Almeria, which was seven points from safety with six games to play.
In other 32nd-round games to be played on Sunday, it's: Levante vs. Hercules; Real Sociedad vs. Sporting Gijon; Deportivo La Coruna vs. Racing Santander; Osasuna vs. Athletic Bilbao; and Espanyol vs. Atletico Madrid.
Villarreal plays Zaragoza on Monday.
