After the Catalan giants edged Rayo Vallecano 1-0 earlier on, Madrid ensured the gap to the champions stayed at four points by beating Diego Simeone's side at the Santiago Bernabeu, reports AFP.
Ademola Lookman put Atletico ahead in the first half but Vinicius and Federico Valverde's strikes gave the hosts the lead soon after the interval.
Nahuel Molina equalised for Atletico, fourth, with a spectacular effort from distance but Vinicius netted again to claim the three points for Los Blancos.
Valverde was sent off for hacking Alex Baena in the final stages but his side held on to win in Alvaro Arbeloa's first derby clash with Atletico since taking over in January.
After ousting Manchester City in the Champions League last 16 on Tuesday, victory against Atletico completed a successful week for Arbeloa and his team.
"We're evolving and working hard so that in games like these Madrid fans can be happy, that the fans can enjoy themselves and that Madrid always win," Vinicius told Real Madrid TV.
"Everyone deserves credit, the coach, the players, the fans, all the work we've done this week. We were sure of our gameplan from the start and that made all the difference."
A pulsating clash began with chances for both sides, with Valverde hitting the post after bursting in behind the Atletico defence.
At the other end, Andriy Lunin, playing in place of the injured Thibaut Courtois, fumbled Marcos Llorente's drive but recovered quickly to grab the loose ball.
Vinicius came close to putting Madrid ahead but Giuliano Simeone blocked twice in quick succession in his own six-yard box from the forward.
Atletico took the lead after 33 minutes with a slick team move, Giuliano Simeone backheeling the ball to Lookman who slotted home.
- Madrid comeback -
Real Madrid netted two quickfire goals early in the second half as Atletico imploded.
Brahim Diaz showed fleet footwork in the area and the unbalanced David Hancko felled the Morocco international.
Vinicius tucked home from the spot in the 52nd minute, sending Juan Musso the wrong way.
Three minutes later and Los Blancos were ahead, with Valverde charging down Jose Gimenez's attempted pass and then firing past Musso with the outside of his boot.
"I think we could have done more, after going a goal up we could have controlled things in a different way," Simeone told reporters.
Atletico pulled level with a brilliant Molina effort, rifled into the top corner from outside the box.
However, Madrid reclaimed the lead through Vinicius once more after Trent Alexander-Arnold fed him, and the Brazilian curled home.
It was Vinicius's 10th goal in his last 11 matches across all competitions, with the forward in superb form.
"I'm very happy because I've worked all season for games like this," added Vinicius.
"When this moment of the season arrives, I don't know why, I always improve."
Julian Alvarez almost levelled once more for Atletico but his effort from the edge of the box crashed back off Lunin's upright.
Arbeloa sent on Jude Bellingham as a substitute for his first appearance since February 1 after a hamstring injury, along with French superstar Kylian Mbappe.
Neither had much of an influence as Madrid were forced to defend after Valverde's foul on Baena bought him a red card.
Madrid protested it was not severe enough of an offence to merit a dismissal, but to no avail.
In 2023 Baena, then at Villarreal, accused Valverde of punching him after a game.
"It's hard to understand..." said Arbeloa of Valverde's red card. "But (afterwards) there were 15 minutes of teamwork, solidarity, defending well and it didn't end up being a problem."
MSH
