Real were cruising after Brazilians Kaka and Marcelo scored first-half goals and Gonzalo Higuain added a third on 64 minutes before Sergio Ramos was shown a straight red for a foul on Sergio Aguero.
Roared on by the home crowd, Diego Forlan pulled a goal back with 11 minutes of regular time left, Aguero added another three minutes later and Iker Casillas produced a superb save to deny the Argentina striker at the death as Real held firm.
Barca have 26 points from 10 matches, Real have 25 and Sevilla, who host Villarreal on Sunday, have 19 in third. Atletico remain in the relegation zone on seven points with just one win.
Pellegrini appeared to be struck by an object thrown from the crowd midway through the second half but played down the incident at the post-match news conference and said he had not suffered any serious injury.
"We had a very good first half and controlled the second until Ramos was sent off," the Chilean said.
"The final minutes were dangerous but did not reflect the superiority we enjoyed throughout the match as a whole."
UNFAMILIAR LINEUP
Barca manager Pep Guardiola fielded an unfamiliar starting lineup at the Nou Camp after consecutive draws against Osasuna and Rubin Kazan, leaving Spain midfielders Xavi and Andres Iniesta on the bench along with Argentina forward Lionel Messi.
The ploy seemed to be paying off when Zlatan Ibrahimovic released Pedro to slot home Barca's first in the 11th minute but they were rocked back nine minutes later when Jose Carlos Nunes headed in from a corner.
Mallorca goalkeeper Dudu Aouate was unlucky to concede a second five minutes before halftime after he produced three reflex saves during a desperate goalmouth scramble to deny Pedro, Henry and Sergio Busquets. But Pedro eventually smashed the ball into the net from close range.
Pedro was again involved in Barca's third four minutes later, floating a freekick to the far post that Busquets nodded back across goal for Henry to head into the empty net.
Messi replaced Pedro in the 51st minute and stroked home a late penalty after Ibrahimovic was chopped down in the area before Alhassane Keita scored a consolation in added time.
"It was an ugly match," Guardiola told a news conference. "It can rain or be cold but wind is the worst. It wasn't one of our best matches but it wasn't bad either."
Deportivo La Coruna made light of having a player sent off in each half earlier on Saturday to win 2-0 at Getafe and climb above Valencia, who entertain promoted Real Zaragoza, on Sunday, into fourth.
Mista nodded the visitors in front in the 15th minute before Miguel Angel Lotina's side went down to 10 men 12 minutes later when striker Riki was shown a second yellow card for what appeared from television replays to be an attempted hand ball. He was earlier booked for diving in the penalty ar
