Lucas Pratto broke the deadlock in the 87th minute when he slotted home substitute Jonathan Copete's low right cross.
"It was the most important (goal) of my career so far. All Boys might have deserved a point and were lucky, but we kept plugging away," Pratto said.
Pratto's strike partner Facundo Ferreyra scored the second three minutes into added time, steering the ball inside the base of the post for his ninth goal of the championship.
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 since Lanus, who had won their previous seven matches, were held 0-0 at home by Estudiantes.
Newell's Old Boys are third with 30 points after coming 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.
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.
"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."
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 "barrabrava" 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.