The 36-year-old striker was perfectly positioned to meet a high cross from the left by Luciano Monzon and lob a neat header into the top corner for Boca's 69th-minute equaliser in a 1-1 draw at Mendoza side Godoy Cruz.
It was Clausura championship leading scorer Palermo's fourth goal in five matches and the first conceded by Boca's opponents.
Godoy Cruz, who would have joined last year's Clausura winners Velez Sarsfield and Colon at the top of the table, had gone ahead in the 23rd minute with a goal by Federico Higuain, brother of the Real Madrid and Argentina striker Gonzalo.
Boca have been trying desperately to pull out of a slump since the middle of last year.
After coach Alfio Basile resigned in January, his successor Abel Alves has tended to rely on younger players and controversially substituted Palermo in a 0-0 draw at home to Atletico Tucuman last weekend.
Palermo's strike partner Lucas Viatri could have won it for Boca but fluffed his chance in front of goal. Boca keeper Javier Garcia then clawed a header from substitute Rodrigo Salinas off the line to secure the point.
Velez, who beat Independiente 3-0, and Colon head the standings on 11 points from five matches, two points more than Godoy Cruz. Boca in 10th place have six points.
Title-holders Banfield, who won the Apertura championship in December, are four points off the pace after a 0-0 draw with bottom team Rosario Central.
Racing Club ended a run of three defeats that cost coach Claudio Vivas his job last week by giving his successor Miguel Angel Russo a winning start, 1-0 at home to San Lorenzo in the weekend's top Buenos Aires derby.
