Palermo, who scored Argentina's winner against Peru in a World Cup qualifier two weeks ago, wore a mask in the first half to protect his broken nose and was rarely involved.
In the second half, having taken the mask off, Palermo received a flicked pass from Juan Roman Riquelme and hit a low shot into the bottom left corner out of Daniel Vega's reach in the 63rd minute.
Palermo had also headed the winner from nearly 40 metres in a 3-2 victory over title holders Velez Sarsfield three weeks ago that launched improved Boca on their present run of four matches without defeat.
Midfielder Marcelo Gallardo had put River ahead after half an hour, curling a brilliant free kick over the wall and into the top left corner past Roberto Abbondanzieri.
Both sides finished with 10 men after River left back Cristian Villagra was sent off a minute into the second half for a second booking, and Boca's Paraguayan defender Julio Cesar Caceres followed in the 50th after upending Ariel Ortega.
Ortega, one of River's three over-33 musketeers with Gallardo and Matias Almeyda, had a penalty saved by Abbondanzieri in the 23rd minute and busy midfielder Matias Abelairas might have snatched victory for the home side but hit the post in the 73rd.
"I think we pardoned them their lives. But the good thing is no one gave anything for us and we played a great match," Abelairas told reporters.
With 15 points after 10 matches, Boca are in 10th place, six points behind new leaders Colon, who beat last week's leaders San Lorenzo 2-1 in a top of the table clash at their Elephants' Cemetery ground in Santa Fe.
LOST MOMENTUM
River, who have only seven points, had the better of the first half but lost momentum in the second when Boca held the upper hand.
It was second "superclasico" in a row to finish 1-1, with both scorers the same, and the fourth without a River win since their last victory two years ago.
A draw was a fair result in a derby that lived up to its billing as the biggest on the Argentine calendar with a 55,000 crowd at the Monumental creating a wall of sound for long spells to a backdrop of red and white banners and streamers, River's colours.
Colon striker Federico Nieto scored both goals as San Lorenzo dug their own grave in Santa Fe.
Saints team mates Renato Civelli and Pablo Pintos argued in the tunnel, Uruguayan Pintos hit Civelli and the referee sent him off.
Nieto, who had opened the scoring with a diving header in the fifth minute, stunned San Lorenzo within two minutes after the restart when he rifled a cross from the right high into the net.
Colon's German Rivarola was sent off in the 57th minute for a bad foul and defender Marcelo Goux scored an own goal in the 75th but they held on for victory.
Velez Sarsfield went down to their first home defeat this year, 2-1 against Newell's Old Boys, who with Estudiantes and Banfield are a point behind Colon.
