Lucas Pratto (pictured) broke the deadlock in the 87th minute when he slotted home Jonathan Copete's low cross, and Facundo Ferreyra made it 2-0 in the third minute of added time, steering the ball inside the post for his ninth goal of the championship.
The winners of the 'Inicial', the first of two championships in Argentina this season, will meeet the winners of the "Final" tournament for the overall title in June.
"It was the most important [goal] of my career so far," said Pratto in a televised interview. "All Boys might have deserved a point and we were lucky, but we kept plugging away."
Velez, chasing their ninth league title and first since the 2010-11 season, lead the first of two championships in the season with 35 points from 17 matches.
They took a two-point advantage over Lanus, who were held 0-0 at home by Estudiantes ending a run of seven wins in a row.
Boca Juniors, who have emerged from a poor spell of form in mid-championship to vie for one of Argentina's Libertadores Cup berths, beat Racing Club 3-1 at home, joining Newell's Old Boys on 30 points. Racing have 29.
Boca, who opened the scoring with defender Matias Caruzzo's header at a corner, settled the match with two fine goals from young midfielder Leandro Paredes before Racing striker Gabriel Hauche pulled one back with a diving header.
'BOCA INCONSISTENT'
"We regret dropping a lot of points, we haven't had a good tournament, we were inconsistent and have paid dearly," said veteran defender Rolando Schiavi, who helped Boca win last season's Apertura title.
"Let's hope we can play the cup next year, that's our objective."
Newell's came from behind to draw 2-2 at Union on Saturday with an equaliser from striker Ignacio Scocco, who scored both goals when Argentina beat Brazil 2-1 in a friendly in Buenos Aires on Wednesday.
Godoy Cruz went down to their fourth consecutive defeat, 2-0 at Tigre, while waiting for the official appointment of their new coach, former Boca Juniors and Argentina striker Martin Palermo.
Independiente's trouble with their "barra brava" hooligan fans continued on Saturday when a group hurled stones at the team bus as it left their Libertadores de America ground after a 2-2 draw with River Plate.
River led 2-1 after an hour but Independiente played better and deserved to win. Instead, they dropped two more points in their desperate fight to stave off relegation for the first time at the end of the season.
