Veteran Martin Palermo confirmed to Argentina coach Diego Maradona his form with one of Boca's goals and, despite also missing a penalty, tied his club's all time goals record of 218 held by Roberto Cherro since 1938.
Not to be left out, Chile defender Gary "Pitbull" Medel popped up on the right to equalize in the 89th minute after Velez had fought back from 3-1 down in the best match of the Argentine season so far.
Midfielder Victor Zapata headed Velez in front from a free-kick after a quarter of an hour of the match at Velez's El Fortin ground in the capital.
Palermo, who had a 26th-minute penalty saved by German Montoya, struck in the 39th from Juan Roman Riquelme's square pass from the left and forward Nicolas Gaitan ended a fine move with a brilliant third just before the hour.
The 29-year-old Uruguayan striker got his second goal, and fifth this year, when he chased a long ball out of defence, shrugged off Boca's Brazilian centre back Luiz Alberto and shot under advancing keeper Javier Garcia to put Velez ahead again.
Medel, who would not have been playing had Chile's World Cup warm-ups on Wednesday not been cancelled because of Saturday's devastating earthquake in his home country, then pounced on the rebound from Montoya, who had dived to save Riquelme's low left-footed shot from outside the box.
