Palermo heads 40-yard winner
Boca ended a run of four defeats to give coach Alfio Basile a boost while arch-rivals River Plate's coach Nestor Gorosito resigned after his team surrendered a lead they had held until the last seven minutes to lose 2-1 at San Lorenzo.
Argentina's big two clubs are well off the championship pace, with Boca eight points behind leaders Estudiantes, who have 16 after seven matches, and River 11 adrift.
Estudiantes are a point clear despite Saturday's 1-0 defeat at Argentinos Juniors, who climbed to second, while title holders Velez dropped to third a point further back, level with Banfield.
San Lorenzo are in a group of four teams on 13 points.
Boca twice equalised after goals by Velez forward Leandro Caruso early in each half - first with midfielder Sebastian Battaglia's diving header after half an hour, then with Juan Roman Riquelme's exquisitely placed drive into the top right corner in the 64th minute.
Ten minutes later Velez goalkeeper German Montoya cleared weakly from the edge of his box down the middle where Palermo headed straight back from more than 35 metres into the unguarded net for his third goal in five days.
The 35-year-old Palermo had already made a case for inclusion in coach Diego Maradona's team on Saturday with both goals in a 2-0 victory for an Argentina team of home-based players against Ghana in a friendly on Wednesday.
Argentina must beat Peru to keep their hopes alive of reaching the 2010 World Cup finals in South Africa.
Gorosito, who has struggled since the start of the season in August to lift his team out of their mediocrity, had hinted in midweek the San Lorenzo game would be his last in charge regardless of the result.
"Having been unable to fulfil the (club's) goals, we preferred with my people (staff) to step to one side," he told reporters confirming his resignation after a club record 16th away match without victory.
Midfielder Diego Buonanotte put River in front after half an hour with a penalty after keeper Pablo Migliore brought down teenage striker Daniel Villalva.
San Lorenzo equalised in the 83rd minute with a penalty by midfielder Leandro Romagnoli after defender Gustavo Cabral punched Jonathan Bottinelli and was sent off.
Striker Bernardo Romeo, a second half substitute, then headed home the winner from Romagnoli's cross four minutes from time.