Messi caught the Atletico defence napping to score with a breathtaking 81st-minute free-kick and secure a 2-1 success for Barca, while an audacious Ronaldo backheel gave Real a 1-0 victory against Madrid neighbours Rayo.
It was a 28th league goal of the campaign for Messi, who succeeded Ronaldo as World Player of the Year and has won the award three times on the trot, leaving him one behind the former Manchester United forward at the top of the La Liga scoring chart.
With 24 of 38 matches played, Jose Mourinho's Real have 64 points, with Pep Guardiola's Barca on 54 in second and Valencia, who lost 2-1 at home to Sevilla on Sunday, 14 points further back in third.
Levante, the lowly Valencia-based club who are this season's surprise package, climbed to fourth on 35 points thanks to their 2-1 win at Espanyol on Saturday, although only eight points separate them from Villarreal in 17th.
Messi's genius settled an intense battle at the Calderon after Atletico's Radamel Falcao had cancelled out Daniel Alves's opening goal.
As the home defence lined up to defend a free-kick wide on the left, Messi noticed Atletico goalkeeper Thibaut Courtois out of position and curled a stunning strike over the Belgian's head into the far top corner.
"We know that it's very difficult, that it's a lot of points, but we are going to keep fighting at every away game and in every match," Guardiola told a news conference.
"At difficult moments, Messi's capacity for leadership always shows, he's been doing it now for four years," he added.
Real's victory at Rayo's tiny stadium in the south east of the Spanish in the earlier kick-off equalled the club record of nine straight away wins from the 2009/10 season.
"I didn't even think when I scored," the Portuguese told reporters.
"I just hit the ball with my heel and therefore surprised the defenders and the goalkeeper," he added.
"I hit it strongly enough so they couldn't stop it. It gave us the victory, so it's worth twice us much to us."
