It was a less happy day for San Lorenzo, whose coach Ramon Diaz resigned after a 1-0 defeat at Tigre.
Palermo's long run looked set to continue as he came close with three chances earlier in the match at the Duco, twice hitting the woodwork and having another saved on the line, before he tapped home fellow striker Pablo Mouche's square ball in the 83rd minute.
"If that last chance hadn't gone in, I'd have had to go," a relieved Palermo told Futbol Para Todos.
Midfielders Cristian Chavez and Nicolas Colazo had given Boca a two-goal lead either side of the interval as the troubled giants, without injured playmaker Juan Roman Riquelme, romped to their best result in 11 matches of the Clausura.
Boca climbed into 14th place in the standings of the season's second championship with 14 points, seven behind leaders Velez Sarsfield, who were upset 3-2 at home by relegation-threatened Quilmes on Saturday.
Palermo, Boca's all time record scorer, took his career tally in all top flight competitions including nine for Argentina to 301.
DIAZ GOES
The Boca faithful were worried by Palermo's lack of goals as he runs down his career at the age of 37. He has eight matches left as he is retiring when the season ends in June.
However, coach Julio Cesar Falcioni did not lose faith in Palermo and had him in all his starting line-ups this year.
San Lorenzo, who made a good start to the championship with four wins in six matches, had gone five without a victory under Diaz in his second spell in charge having steered them to the Clausura title in 2007.
"I assume full responsibility for what has happened. We have failed as a coaching staff and as everything depends on results I can't carry on in this situation," Diaz told reporters.
"I'm used to fighting at the top (of the standings) and we've lost our chances."
The Saints, who according to media reports tried to persuade Diaz to stay on at least until next weekend's "clasico" at home to Huracan, are mid-table with 15 points from 11 matches.
Diaz is the fifth coach to have left his job during the Clausura.
