The Manchester City midfielder opened the scoring from the spot in the 12th minute after electric winger Yamal tumbled in the box and Dani Olmo extended Spain’s lead with a fine individual goal.
A mistake by Spain goalkeeper Unai Simon allowed Rodrygo to pull one back before the break and teen sensation Endrick, on as a substitute, fired Brazil level five minutes into the second half.
Rodri dispatched his second spot-kick late on after Dani Carvajal was clipped by Lucas Beraldo but Paqueta had the final say.
The match, arranged to help combat racism after various incidents of abuse aimed at Real Madrid and Brazil winger Vinicius Junior in Spain, proved a pulsating battle between two of football’s heavyweight nations.
Vinicius captained Brazil for the first time but was largely kept quiet, with his teenage compatriot and future Los Blancos team-mate Endrick continuing to enjoy the limelight, along with Barcelona youngster Yamal.
“It’s a shame it got away from us in the last second, it was a penalty we could have avoided,” Rodri told Teledeporte.
Rodri was given the armband on this occasion by regular skipper Alvaro Morata, as a gesture for the recent death of the midfielder’s grandfather.
“I dedicated (the goals) to my grandfather, for everything that he taught me,” added Rodri.
La Roja excelled in the first half, barely allowing five-time World Cup winners Brazil a sniff in Selecao coach Dorival Junior’s second match at the helm.
“I’m angry not to win a game in which we were superior,” admitted Spain coach Luis de la Fuente, but he said he was encouraged ahead of Euro 2024 this summer.
“The positive thing … is that we have come out reinforced, the team is growing and giving the feeling that this side can go very far.”
‘One of the greats’
Yamal won the penalty converted by Rodri for the opening goal, although the Barcelona winger was fortunate after tumbling easily under a challenge from Joao Gomes.
The 16-year-old continues to grow in stature with every match and played in Olmo for the second goal, who finished well after sublime footwork.
“(Yamal) had a brilliant performance, but I like to be careful, that’s the best we can give these youngsters,” said De la Fuente.
Spain allowed Brazil into the match just before half-time when Simon gave the ball away carelessly to Rodrygo who pounced with a lob.
At half-time Dorival brought on Endrick, who scored the winner against England on Saturday in another friendly, for his first appearance at the home of his future club, Real Madrid.
The 17-year-old starlet did not wait long to net his first goal in the Spanish capital, volleying home after a corner was headed into his path.
“If he completes his development he will be one of the greats,” said Dorival.
Spain thought they had won when Rodri slammed in his second penalty in the final stages after Carvajal hit the deck in a collision with Beraldo, but Brazil refused to throw in the towel.
The visitors earned a penalty of their own deep in stoppage time when Carvajal, having fallen, cynically pulled back Galeno’s leg.
Paqueta, who was earlier lucky to survive without punishment for swinging an arm at Marc Cucurella, sent Simon the wrong way to equalise with virtually the last kick.
“A game against Brazil is never friendly, both sides want to win, we gave everything on the pitch with and without the ball,” said Olmo.
“In the end it didn’t happen, but we have to be proud of what we did.”
© Agence France-Presse
Photo: Twitter @CFC_Janty